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Abstract The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota–host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders investigation of respiratory microbiota. Here, we performed a pilot study to assess the suitability of the NAxtra nucleic acid extraction protocol for profiling bacterial microbiota in respiratory samples. A small number of nasopharyngeal aspirate (n = 8), nasal swab (n = 8), and saliva samples (n = 8) were collected, nucleic acids were isolated using the NAxtra protocol, and 16 S rRNA gene sequencing was performed to characterize bacterial microbiota, which were compared to the same sample types from previous studies using other protocols. The bacterial composition in nasal and saliva samples were consistent with previous reports. Saliva microbiota was significantly richer than nasal microbiota and varied less among individual samples than nasal microbiota. Bacterial composition in nasal samples was distinct from nasopharyngeal aspirates, but closer to saliva samples. A sequencing depth of 50,000 reads/sample was sufficient for microbiota profiling in low biomass respiratory samples. Our pilot study indicates the potential of the NAxtra protocol for bacterial microbiota characterization of low-microbial biomass samples and supports a more comprehensive study to fully evaluate the value of the NAxtra protocol in microbiota research and clinical diagnostics of respiratory pathogens.

Abstract Our species and other hominins have used earth mineral pigments since at least ~500,000 years ago, if not earlier. Its preservation and ubiquity within archaeological records across sub-Saharan Africa are well documented, but regional-scale networks of mineral selection, mining, transport, and use is an underdeveloped field. Here, we present a framework for interpreting regional variations within an overarching ochre-behavioral community of practice. Deep-time records of ochre provisioning span the final Middle Stone Age and Late Stone Age in modern day Eswatini, revealing longstanding cultural continuities in the intergenerational transmission of shared knowledge on landscapes, geology, and the desired physicochemical properties of mineral pigments. These communities of practice did not develop in isolation, and were part of a wider system of relations that were influenced and mediated by social interactions, such as technological learning, seasonal traveling, material culture exchange, and symbolic expression. We use compositional analyses to determine localized ochre procurement strategies and long-distance transport across a network of fifteen archaeological sites and mineral resources. Newly refined chronologies from Lion Cavern at Ngwenya using optically stimulated luminescence dating also reaffirm its antiquity as the oldest known evidence for intensive ochre mining worldwide (~48,000 years ago).

Modelling catalytic fixed bed reactors with a small tube-to-particle diameter ratio requires a detailed description of the interactions between fluid flow, intra-particle transport, and the chemical reaction(s) within the catalyst. Particle-resolved computational fluid dynamics (PRCFD) simulations are the most promising approach to predict the behaviour of these reactors accurately, since they take into account the local packed bed structure explicitly. In this work, a conjugated heat and mass transfer model for use in PRCFD simulations is presented in order to couple the fluid flow through the fixed bed with transport and reaction in the porous catalyst, while guaranteeing the no-slip boundary condition at the fluid–solid interface. For this purpose, the solutions of the solid and fluid domain are computed separately and are coupled by calculation and updating the boundary condition at the particle surface. Owing to the consideration of secondary gradients, the developed transfer model is also valid for unstructured calculation meshes containing non-orthogonal cells at the fluid–solid interface. Such meshes are often used to resolve complex geometries, such as a packed bed, in a computationally efficient manner. The coupling approach is validated using cases for which an analytical solution or literature correlations derived from experimental data are available. The simulation results of a short catalytic packed bed with rings catalysing the partial oxidation of n-butane to maleic anhydride exemplify the potential of PRCFD involving reactions to analyse the catalyst performance in great detail.

We present a series of 12 OSL/IRSL dates that revise and complete the chronology of the important Middle (MSA) and Later Stone Age (LSA) site Umbeli Belli in KwaZulu-Natal, South Africa. These dates shift the previous radiometric ages thousands of years older than earlier measurements and play a key role in revising the cultural stratigraphy of KwaZulu-Natal. We also discuss how these dates bring the chrono- and cultural stratigraphy of southern Africa into clearer focus. The Robberg sequence of Umbeli Belli is now firmly dated to 21 ± 2 ka, whereas the preceding Early LSA assemblage dates to ~32 ka, representing one of the earliest dates for this cultural expression in the broader region. The final MSA assemblages from Layer 7 to 9 now date to between 35 ka and 40 ka, overlapping more tightly with comparable assemblages from Sibhudu, Umhlatuzana and other sites. Layer 10, which was previously also assigned to the final MSA, now dates to ~47–54 ka, placing the assemblage within the temporal range of the Late MSA. The new dates provide a good explanation for the clear differences in material culture between Layer 10 and the younger layers. We also present two new ages for the deeper horizons 11b and 12 at Umbeli Belli, dating to 76 ± 9 ka and 80 ± 9 ka, respectively. Significance: • Revised and new age estimates are given for the Middle and Later Stone Age sequence of Umbeli Belli. • These age changes allow new comparisons with nearby prehistoric sites. • They change our view of the regional variability of technologies and cultures between ca. 80 and 20 ka on the east coast of South Africa.

Abstract Background Circulating extracellular vesicles (EVs) are increased in preeclampsia (PE) and are associated with severity and progression. We examined in this exploratory cohort study if the mRNAs and long noncoding RNAs (lncRNAs) in plasma-derived EVs were dysregulated in PE compared to normal pregnancy and display different temporal patterns during gestation. Methods We isolated EVs from plasma at weeks 22–24 and 36–38 in women with and without PE (n=7 in each group) and performed RNA-seq, focusing on mRNAs and lncRNAs. We validated highly expressed mitochondrial and platelet-derived RNAs discovered from central pathways in 60 women with/without PE. We examined further one of the regulated RNAs, noncoding mitochondrially encoded tRNA alanine (MT-TA), in leukocytes and plasma to investigate its biomarker potential and association with clinical markers of PE. Results We found abundant levels of platelet-derived and mitochondrial RNAs in EVs. Expression of these RNAs were decreased and lncRNAs increased in EVs from PE compared to without PE. These findings were further validated by qPCR for mitochondrial RNAs MT-TA, MT-ND2, MT-CYB and platelet-derived RNAs PPBP, PF4, CLU in EVs. Decreased expression of mitochondrial tRNA MT-TA in leukocytes at 22–24 weeks was strongly associated with the subsequent development of PE. Conclusions Platelet-derived and mitochondrial RNA were highly expressed in plasma EVs and were decreased in EVs isolated from women with PE compared to without PE. LncRNAs were mostly increased in PE. The MT-TA in leukocytes may be a useful biomarker for prediction and/or early detection of PE. Graphical Abstract

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

Abstract Background Novel commercial kits for whole genome library preparation for next-generation sequencing on Illumina platforms promise shorter workflows, lower inputs and cost savings. Time savings are achieved by employing enzymatic DNA fragmentation and by combining end-repair and tailing reactions. Fewer cleanup steps also allow greater DNA input flexibility (1 ng-1 μg), PCR-free options from 100 ng DNA, and lower price as compared to the well-established sonication and tagmentation-based DNA library preparation kits. Results We compared the performance of four enzymatic fragmentation-based DNA library preparation kits (from New England Biolabs, Roche, Swift Biosciences and Quantabio) to a tagmentation-based kit (Illumina) using low input DNA amounts (10 ng) and PCR-free reactions with 100 ng DNA. With four technical replicates of each input amount and kit, we compared the kits’ fragmentation sequence-bias as well as performance parameters such as sequence coverage and the clinically relevant detection of single nucleotide and indel variants. While all kits produced high quality sequence data and demonstrated similar performance, several enzymatic fragmentation methods produced library insert sizes which deviated from those intended. Libraries with longer insert lengths performed better in terms of coverage, SNV and indel detection. Lower performance of shorter-insert libraries could be explained by loss of sequence coverage to overlapping paired-end reads, exacerbated by the preferential sequencing of shorter fragments on Illumina sequencers. We also observed that libraries prepared with minimal or no PCR performed best with regard to indel detection. Conclusions The enzymatic fragmentation-based DNA library preparation kits from NEB, Roche, Swift and Quantabio are good alternatives to the tagmentation based Nextera DNA flex kit from Illumina, offering reproducible results using flexible DNA inputs, quick workflows and lower prices. Libraries with insert DNA fragments longer than the cumulative sum of both read lengths avoid read overlap, thus produce more informative data that leads to strongly improved genome coverage and consequently also increased sensitivity and precision of SNP and indel detection. In order to best utilize such enzymatic fragmentation reagents, researchers should be prepared to invest time to optimize fragmentation conditions for their particular samples.

Abstract The gene ankyrin-3 (ANK3) has been consistently associated with bipolar disorder (BD) in several genome-wide association studies (GWAS). The exact molecular mechanisms underlying this genetic association remain unknown. The discovery of a loss-of-function variant (rs41283526*G) in an alternatively spliced exon (ENSE00001786716) with a protective effect, suggested that elevated expression of this particular isoform could be a risk factor for developing the disorder. We developed a novel approach for measuring the expression level of all splice forms at a challenging genetic locus using a combination of droplet digital PCR and high-throughput sequencing of indexed PCR amplicons. The combined method was performed on a large collection of 568 postmortem brain samples of BD and SCZ cases and controls. We also studied the expression of the splice forms in a child-development cohort of 41 healthy males. We found that our approach can quantify the splice forms in brain samples, although with less precision than ddPCR. We detected highly significant differences in expression of splice forms and transcription start sites between brain regions, notably with higher expression of the BD-associated isoform in the corpus callosum compared to frontal tissue (mean fold change = 1.80, p

In 1952, Gordon Cramb published the first report on his excavations at Holley Shelter, in KwaZulu-Natal, South Africa. Although Cramb’s work implied organic preservation associated with a unique stone tool assemblage from a Middle Stone Age (MSA) context, Holley Shelter disappeared from the archaeological landscape until 2015, when we provided a reinvestigation of the lithic assemblages from the 1950s. Our study indicated a tentative chronological framework around Marine Isotope Stage 3 (MIS3) for the human occupation of the site. However, Cramb’s excavations did not produce reliable chronometric ages and the botanical and zoological finds from Holley Shelter remain for the most part unstudied. This is problematic as the site constitutes one of the few inland MSA rock shelters of KwaZulu-Natal featuring organic preservation. In 2022, 70 years after Cramb’s first report, we started a new research project focusing on renewed excavations to obtain archaeological remains from a controlled stratigraphy, absolute chronometric ages and reliable data on the palaeoenvironment at the border between the coastal belt and the midlands of KwaZulu-Natal. Here, we provide initial results from the first field campaign in 2022 on the stratigraphic sequence and archaeological finds and discuss their implications for future multidisciplinary research. Significance: • Environmental change can have a strong impact on hunter-gatherer behaviour, migration and technological choices. It is thus crucial to contextualise archaeological material with a strong palaeoenvironmental record. • The inland of KwaZulu-Natal, South Africa, represents an understudied region in terms of Stone Age archaeological sites and palaeoenvironmental record. • Holley Shelter is one of the few sites in South Africa with excellent organic preservation and a deep stratigraphic record, which provide a great opportunity to investigate human-landscape interaction and technological change throughout the Middle and Later Stone Age.

Abstract With the technological advances in 3D printing technology, which are associated with ever-increasing printing resolution, additive manufacturing is now increasingly being used for rapid manufacturing of complex devices including microsystems development for laboratory applications. Personalized experimental devices or entire bioreactors of high complexity can be manufactured within few hours from start to finish. This study presents a customized 3D-printed micro bubble column reactor (3D-µBCR), which can be used for the cultivation of microorganisms (e.g., Saccharomyces cerevisiae) and allows online-monitoring of process parameters through integrated microsensor technology. The modular 3D-µBCR achieves rapid homogenization in less than 1 s and high oxygen transfer with k L a values up to 788 h−1 and is able to monitor biomass, pH, and DOT in the fluid phase, as well as CO2 and O2 in the gas phase. By extensive comparison of different reactor designs, the influence of the geometry on the resulting hydrodynamics was investigated. In order to quantify local flow patterns in the fluid, a three-dimensional and transient multiphase Computational Fluid Dynamics model was successfully developed and applied. The presented 3D-µBCR shows enormous potential for experimental parallelization and enables a high level of flexibility in reactor design, which can support versatile process development.

The use of marine resources and the settlement of coastal settlements may have influenced the bio-cultural evolution and dispersal of Pleistocene Homo sapiens in Africa. In order to test such scenarios, however, we require evidence for these behaviours deriving from an expanded spatio-temporal archaeological record. The Stone Age of South Africa documents the richest and longest record of coastal adaptations. In contrast to abundant evidence of coastal sites on the western and southern seaboard, the eastern Indian Ocean coast has not played a role in recent discussions. Considering the important and well-known Middle and Later Stone Age (MSA/LSA) record from inland sites of KwaZulu-Natal (KZN), this region may be an underappreciated area for further study. Here we provide a systematic overview of marine resource use and the settlement of coastal landscapes during the Late Pleistocene and Holocene in KZN. For the first time, we contextualize these archaeological findings with a review and new data on the changing marine and coastal geomorphology in the context of GIS modelling and offshore marine geophysical investigations. Our review finds evidence for long-term dietary and non-dietary use of marine resources during the MSA and LSA from a few stratified sites, with many more surface occurrences particularly for the MSA along the modern KZN coastline indicating human habitation. Comparisons to other areas of South Africa, GIS modelling and geological considerations suggest that current data on the eastern seaboard are not reflective of the original extent and nature of the consumption of marine foods and settlement of coastal landscapes. By contextualizing the biased and patchy MSA and LSA record with results on the dynamic marine and coastal geomorphology of KZN, we develop productive lines of future studies to assess open questions on potential coastal adaptations in this region. These research strategies include the identification of areas with high potential for finding new sites within a 10 km transect along the current coastline as well as dedicated off-shore projects including underwater archaeology aided by new marine geological work in the southwest Indian Ocean.

Particle-resolved computational fluid dynamics (PRCFD) is the most detailed modeling approach for fixed bed reactors. A major issue of PRCFD is to ensure a high quality of the underlying 3D calculation mesh around the particle-particle and particle-wall contacts, which otherwise results in convergence problems. A still unresolved challenge, especially for packed beds of non-spherical particles, is to avoid this poor-quality mesh at contacts by modification of the packed bed geometry, while providing a reasonable number of mesh cells and physical accuracy. Based on the so called local caps method, a novel mesh-type independent routine was developed to modify all occurring contacts of a packed bed of rings and to generate a computationally efficient high-quality mesh. Thereby, one of the two particles involved in a point or line contact was inflated and used as cap geometry, whereas area contacts were combined via the contact surface. The impact of the cap size on mesh quality, packed bed structure, fluid flow and heat transport was investigated for a technically relevant slender packed bed under various conditions. For a small ratio between solid and fluid thermal conductivity (λPλF≤23.1), and ReP=50−600, a cap size smaller than 0.8% of the outer particle diameter did not have significant impact on the simulation results. To apply the approach to other packing structures and particle shapes, it is recommended to investigate at least three different cap sizes to determine at which cap size the independence from contact modification is achieved.

Abstract Background Yeast infections are often connected with formation of biofilms that are extremely difficult to eradicate. An excellent model system for deciphering multifactorial determinants of yeast biofilm development is the colony biofilm, composed of surface (“aerial”) and invasive (“root”) cells. While surface cells have been partially analyzed before, we know little about invasive root cells. In particular, information on the metabolic, chemical and morphogenetic properties of invasive versus surface cells is lacking. In this study, we used a new strategy to isolate invasive cells from agar and extracellular matrix, and employed it to perform genome wide expression profiling and biochemical analyses of surface and invasive cells. Results RNA sequencing revealed expression differences in 1245 genes with high statistical significance, indicating large genetically regulated metabolic differences between surface and invasive cells. Functional annotation analyses implicated genes involved in stress defense, peroxisomal fatty acid β-oxidation, autophagy, protein degradation, storage compound metabolism and meiosis as being important in surface cells. In contrast, numerous genes with functions in nutrient transport and diverse synthetic metabolic reactions, including genes involved in ribosome biogenesis, biosynthesis and translation, were found to be important in invasive cells. Variation in gene expression correlated significantly with cell-type specific processes such as autophagy and storage compound accumulation as identified by microscopic and biochemical analyses. Expression profiling also provided indications of cell-specific regulations. Subsequent knockout strain analyses identified Gip2p, a regulatory subunit of type 1 protein phosphatase Glc7p, to be essential for glycogen accumulation in surface cells. Conclusions This is the first study reporting genome wide differences between surface and invasive cells of yeast colony biofilms. New findings show that surface and invasive cells display very different physiology, adapting to different conditions in different colony areas and contributing to development and survival of the colony biofilm as a whole. Notably, surface and invasive cells of colony biofilms differ significantly from upper and lower cells of smooth colonies adapted to plentiful laboratory conditions.

Abstract Background Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. Methods We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. Results The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Conclusions Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.

Transcriptomic profiling of the immune response induced by vaccine adjuvants is of critical importance for the rational design of vaccination strategies. In this study, transcriptomics was employed to profile the effect of the vaccine adjuvant used for priming on the immune response following re-exposure to the vaccine antigen alone. Mice were primed with the chimeric vaccine antigen H56 of Mycobacterium tuberculosis administered alone or with the CAF01 adjuvant and boosted with the antigen alone. mRNA sequencing was performed on blood samples collected 1, 2, and 7 days after priming and after boosting. Gene expression analysis at day 2 after priming showed that the CAF01 adjuvanted vaccine induced a stronger upregulation of the innate immunity modules compared with the unadjuvanted formulation. The immunostimulant effect of the CAF01 adjuvant, used in the primary immunization, was clearly seen after a booster immunization with a low dose of antigen alone. One day after boost, we observed a strong upregulation of multiple genes in blood of mice primed with H56 + CAF01 compared with mice primed with the H56 alone. In particular, blood transcription modules related to innate immune response, such as monocyte and neutrophil recruitment, activation of antigen-presenting cells, and interferon response were activated. Seven days after boost, differential expression of innate response genes faded while a moderate differential expression of T cell activation modules was appreciable. Indeed, immunological analysis showed a higher frequency of H56-specific CD4+ T cells and germinal center B cells in draining lymph nodes, a strong H56-specific humoral response and a higher frequency of antibody-secreting cells in spleen of mice primed with H56 + CAF01. Taken together, these data indicate that the adjuvant used for priming strongly reprograms the immune response that, upon boosting, results in a stronger recall innate response essential for shaping the downstream adaptive response.

MicroRNA (miRNA) transfer via exosomes may mediate cell-to-cell communication. Interestingly, specific miRNAs are enriched in exosomes in a cell-type-dependent fashion. However, the mechanisms whereby miRNAs are sorted to exosomes and the significance of miRNA transfer to acceptor cells are unclear. We used macrophages and endothelial cells (ECs) as a model of heterotypic cell communication in order to investigate both processes. RNA profiling of macrophages and their exosomes shows that miRNA sorting to exosomes is modulated by cell-activation-dependent changes of miRNA target levels in the producer cells. Genetically perturbing the expression of individual miRNAs or their targeted transcripts promotes bidirectional miRNA relocation from the cell cytoplasm/P bodies (sites of miRNA activity) to multivesicular bodies (sites of exosome biogenesis) and controls miRNA sorting to exosomes. Furthermore, the use of Dicer-deficient cells and reporter lentiviral vectors (LVs) for miRNA activity shows that exosomal miRNAs are transferred from macrophages to ECs to detectably repress targeted sequences.

A common reactor type in the chemical and process industry is the fixed-bed reactor. Accurate modeling can be achieved with particle-resolved computational fluid dynamic (CFD) simulations. However, the underlying bed morphology plays a paramount role. Synthetic bed-generation methods are much more flexible and faster than image-based approaches. In this study, we look critically at the two different bed generation methods: Discrete element method (DEM) (in the commercial software STAR-CCM+) and the rigid-body model (in the open-source software Blender). The two approaches are compared in terms of synthetically generated beds with experimental data of overall and radial porosity, particle orientation, as well as radial velocities. Both models show accurate agreement for the porosity. However, only Blender shows similar particle orientation than the experimental results. The main drawback of the DEM is the long calculation time and the shape approximation with composite particles.

Expression of the mannose receptor (MRC1/CD206) identifies macrophage subtypes, such as alternatively activated macrophages (AAMs) and M2-polarized tumor-associated macrophages (TAMs), which are endowed with tissue-remodeling, proangiogenic, and protumoral activity. However, the significance of MRC1 expression for TAM's protumoral activity is unclear. Here, we describe and characterize miR-511-3p, an intronic microRNA (miRNA) encoded by both mouse and human MRC1 genes. By using sensitive miRNA reporter vectors, we demonstrate robust expression and bioactivity of miR-511-3p in MRC1+ AAMs and TAMs. Unexpectedly, enforced expression of miR-511-3p tuned down the protumoral gene signature of MRC1+ TAMs and inhibited tumor growth. Our findings suggest that transcriptional activation of Mrc1 in TAMs evokes a genetic program orchestrated by miR-511-3p, which limits rather than enhances their protumoral functions. Besides uncovering a role for MRC1 as gatekeeper of TAM's protumoral genetic programs, these observations suggest that endogenous miRNAs may operate to establish thresholds for inflammatory cell activation in tumors.

Studies of the African Middle Stone Age (MSA) have become central for defining the cultural adaptations that accompanied the evolution of modern humans. While much of recent research in South Africa has focused on the Still Bay and Howiesons Poort (HP), periods following these technocomplexes were often neglected. Here we examine lithic assemblages from Sibudu that post-date the HP to further the understanding of MSA cultural variability during the Late Pleistocene. Sibudu preserves an exceptionally thick, rich, and high-resolution archaeological sequence that dates to ∼ 58 ka, which has recently been proposed as type assemblage for the "Sibudan". This study presents a detailed analysis of the six uppermost lithic assemblages from these deposits (BM-BSP) that we excavated from 2011-2013. We define the key elements of the lithic technology and compare our findings to other assemblages post-dating the HP. The six lithic assemblages provide a distinct and robust cultural signal, closely resembling each other in various technological, techno-functional, techno-economic, and typological characteristics. These results refute assertions that modern humans living after the HP possessed an unstructured and unsophisticated MSA lithic technology. While we observed several parallels with other contemporaneous MSA sites, particularly in the eastern part of southern Africa, the lithic assemblages at Sibudu demonstrate a distinct and so far unique combination of techno-typological traits. Our findings support the use of the Sibudan to help structuring this part of the southern African MSA and emphasize the need for further research to identify the spatial and temporal extent of this proposed cultural unit.

Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5' and 3'-ends of sequencing reads. The palindromic sequences themselves have specific properties - the bases at the 5'-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3'-end. The terminal 3' bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3'-end of DNA strands, with the 5'-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias.

Lassa virus (LASV) causes deadly hemorrhagic fever disease for which there are no vaccines and limited treatments. LASV-encoded L polymerase is required for viral RNA replication and transcription. The functional domains of L-a large protein of 2218 amino acid residues-are largely undefined, except for the centrally located RNA-dependent RNA polymerase (RdRP) motif. Recent structural and functional analyses of the N-terminal region of the L protein from lymphocytic choriomeningitis virus (LCMV), which is in the same Arenaviridae family as LASV, have identified an endonuclease domain that presumably cleaves the cap structures of host mRNAs in order to initiate viral transcription. Here we present a high-resolution crystal structure of the N-terminal 173-aa region of the LASV L protein (LASV L173) in complex with magnesium ions at 1.72 Å. The structure is highly homologous to other known viral endonucleases of arena- (LCMV NL1), orthomyxo- (influenza virus PA), and bunyaviruses (La Crosse virus NL1). Although the catalytic residues (D89, E102 and K122) are highly conserved among the known viral endonucleases, LASV L endonuclease structure shows some notable differences. Our data collected from in vitro endonuclease assays and a reporter-based LASV minigenome transcriptional assay in mammalian cells confirm structural prediction of LASV L173 as an active endonuclease. The high-resolution structure of the LASV L endonuclease domain in complex with magnesium ions should aid the development of antivirals against lethal Lassa hemorrhagic fever.

Dosage compensation in male Drosophila relies on the X chromosome-specific recruitment of a chromatin-modifying machinery, the dosage compensation complex (DCC). The principles that assure selective targeting of the DCC are unknown. According to a prevalent model, X chromosome targeting is initiated by recruitment of the DCC core components, MSL1 and MSL2, to a limited number of so-called "high-affinity sites" (HAS). Only very few such sites are known at the DNA sequence level, which has precluded the definition of DCC targeting principles. Combining RNA interference against DCC subunits, limited crosslinking, and chromatin immunoprecipitation coupled to probing high-resolution DNA microarrays, we identified a set of 131 HAS for MSL1 and MSL2 and confirmed their properties by various means. The HAS sites are distributed all over the X chromosome and are functionally important, since the extent of dosage compensation of a given gene and its proximity to a HAS are positively correlated. The sites are mainly located on non-coding parts of genes and predominantly map to regions that are devoid of nucleosomes. In contrast, the bulk of DCC binding is in coding regions and is marked by histone H3K36 methylation. Within the HAS, repetitive DNA sequences mainly based on GA and CA dinucleotides are enriched. Interestingly, DCC subcomplexes bind a small number of autosomal locations with similar features.

The dosage compensation complex (DCC) in Drosophila melanogaster is responsible for up-regulating transcription from the single male X chromosome to equal the transcription from the two X chromosomes in females. Visualization of the DCC, a large ribonucleoprotein complex, on male larval polytene chromosomes reveals that the complex binds selectively to many interbands on the X chromosome. The targeting of the DCC is thought to be in part determined by DNA sequences that are enriched on the X. So far, lack of knowledge about DCC binding sites has prevented the identification of sequence determinants. Only three binding sites have been identified to date, but analysis of their DNA sequence did not allow the prediction of further binding sites. We have used chromatin immunoprecipitation to identify a number of new DCC binding fragments and characterized them in vivo by visualizing DCC binding to autosomal insertions of these fragments, and we have demonstrated that they possess a wide range of potential to recruit the DCC. By varying the in vivo concentration of the DCC, we provide evidence that this range of recruitment potential is due to differences in affinity of the complex to these sites. We were also able to establish that DCC binding to ectopic high-affinity sites can allow nearby low-affinity sites to recruit the complex. Using the sequences of the newly identified and previously characterized binding fragments, we have uncovered a number of short sequence motifs, which in combination may contribute to DCC recruitment. Our findings suggest that the DCC is recruited to the X via a number of binding sites of decreasing affinities, and that the presence of high- and moderate-affinity sites on the X may ensure that lower-affinity sites are occupied in a context-dependent manner. Our bioinformatics analysis suggests that DCC binding sites may be composed of variable combinations of degenerate motifs.

The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota–host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders investigation of respiratory microbiota. Here, we performed a pilot study to assess the suitability of the NAxtra nucleic acid extraction protocol for profiling bacterial microbiota in respiratory samples. A small number of nasopharyngeal aspirate (n = 8), nasal swab (n = 8), and saliva samples (n = 8) were collected, nucleic acids were isolated using the NAxtra protocol, and 16 S rRNA gene sequencing was performed to characterize bacterial microbiota, which were compared to the same sample types from previous studies using other protocols. The bacterial composition in nasal and saliva samples were consistent with previous reports. Saliva microbiota was significantly richer than nasal microbiota and varied less among individual samples than nasal microbiota. Bacterial composition in nasal samples was distinct from nasopharyngeal aspirates, but closer to saliva samples. A sequencing depth of 50,000 reads/sample was sufficient for microbiota profiling in low biomass respiratory samples. Our pilot study indicates the potential of the NAxtra protocol for bacterial microbiota characterization of low-microbial biomass samples and supports a more comprehensive study to fully evaluate the value of the NAxtra protocol in microbiota research and clinical diagnostics of respiratory pathogens. [ABSTRACT FROM AUTHOR]

Single‐particle reactors in lab‐scale are a promising technology to gain an in‐depth understanding of the intricate reaction and transport processes that occur in catalyst particles under operando conditions. It is not described whether the effect of the bounding walls in such narrow flow channels influence the processes at the particle. Therefore, this work applies three‐dimensional (3D) computational fluid dynamics (CFD) simulations to analyze the drag coefficient CD alongside the local and average particle Nusselt number Nup as characteristic local and integral quantities in the range of particle Reynolds numbers 10 ≤ Rep ≤ 103. An equation is derived to correct for the wall effects on CD and Nup and assist the experimenter in the interpretation of measured results. [ABSTRACT FROM AUTHOR]

Modelling catalytic fixed bed reactors with a small tube-to-particle diameter ratio requires a detailed description of the interactions between fluid flow, intra-particle transport, and the chemical reaction(s) within the catalyst. Particle-resolved computational fluid dynamics (PRCFD) simulations are the most promising approach to predict the behaviour of these reactors accurately, since they take into account the local packed bed structure explicitly. In this work, a conjugated heat and mass transfer model for use in PRCFD simulations is presented in order to couple the fluid flow through the fixed bed with transport and reaction in the porous catalyst, while guaranteeing the no-slip boundary condition at the fluid–solid interface. For this purpose, the solutions of the solid and fluid domain are computed separately and are coupled by calculation and updating the boundary condition at the particle surface. Owing to the consideration of secondary gradients, the developed transfer model is also valid for unstructured calculation meshes containing non-orthogonal cells at the fluid–solid interface. Such meshes are often used to resolve complex geometries, such as a packed bed, in a computationally efficient manner. The coupling approach is validated using cases for which an analytical solution or literature correlations derived from experimental data are available. The simulation results of a short catalytic packed bed with rings catalysing the partial oxidation of n-butane to maleic anhydride exemplify the potential of PRCFD involving reactions to analyse the catalyst performance in great detail. [ABSTRACT FROM AUTHOR]

Our species and other hominins have used earth mineral pigments since at least ~500,000 years ago, if not earlier. Its preservation and ubiquity within archaeological records across sub-Saharan Africa are well documented, but regional-scale networks of mineral selection, mining, transport, and use is an underdeveloped field. Here, we present a framework for interpreting regional variations within an overarching ochre-behavioral community of practice. Deep-time records of ochre provisioning span the final Middle Stone Age and Late Stone Age in modern day Eswatini, revealing longstanding cultural continuities in the intergenerational transmission of shared knowledge on landscapes, geology, and the desired physicochemical properties of mineral pigments. These communities of practice did not develop in isolation, and were part of a wider system of relations that were influenced and mediated by social interactions, such as technological learning, seasonal traveling, material culture exchange, and symbolic expression. We use compositional analyses to determine localized ochre procurement strategies and long-distance transport across a network of fifteen archaeological sites and mineral resources. Newly refined chronologies from Lion Cavern at Ngwenya using optically stimulated luminescence dating also reaffirm its antiquity as the oldest known evidence for intensive ochre mining worldwide (~48,000 years ago). Mineral pigments have been used by humans and human ancestors for at least 500 thousand years. Here, the authors document ochre provisioning in Middle and Late Stone Age Eswatini, demonstrate the presence of transport networks across 15 sites, and suggest that Lion Cavern is the oldest intensive ochre mine. [ABSTRACT FROM AUTHOR]