TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7-9.

Toll-like receptors (TLRs) have a crucial role in the recognition of pathogens and initiation of immune responses1-3. Here we show that a previously uncharacterized protein encoded by CXorf21-a gene that is associated with systemic lupus erythematosus4,5-interacts with the endolysosomal transporter SLC15A4, an essential but poorly understood component of the endolysosomal TLR machinery also linked to autoimmune disease4,6-9. Loss of this type-I-interferon-inducible protein, which we refer to as 'TLR adaptor interacting with SLC15A4 on the lysosome' (TASL), abrogated responses to endolysosomal TLR agonists in both primary and transformed human immune cells. Deletion of SLC15A4 or TASL specifically impaired the activation of the IRF pathway without affecting NF-κB and MAPK signalling, which indicates that ligand recognition and TLR engagement in the endolysosome occurred normally. Extensive mutagenesis of TASL demonstrated that its localization and function relies on the interaction with SLC15A4. TASL contains a conserved pLxIS motif (in which p denotes a hydrophilic residue and x denotes any residue) that mediates the recruitment and activation of IRF5. This finding shows that TASL is an innate immune adaptor for TLR7, TLR8 and TLR9 signalling, revealing a clear mechanistic analogy with the IRF3 adaptors STING, MAVS and TRIF10,11. The identification of TASL as the component that links endolysosomal TLRs to the IRF5 transcription factor via SLC15A4 provides a mechanistic explanation for the involvement of these proteins in systemic lupus erythematosus12-14.

A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability.

While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.

RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data.

Assessing the quality of sequencing data plays a crucial role in downstream data analysis. However, existing tools often achieve sub-optimal efficiency, especially when dealing with compressed files or performing complicated quality control operations such as over-representation analysis and error correction. We present RabbitQCPlus, an ultra-efficient quality control tool for modern multi-core systems. RabbitQCPlus uses vectorization, memory copy reduction, parallel (de)compression, and optimized data structures to achieve substantial performance gains. It is 1.1 to 5.4 times faster when performing basic quality control operations compared to state-of-the-art applications yet requires fewer compute resources. Moreover, RabbitQCPlus is at least 4 times faster than other applications when processing gzip-compressed FASTQ files and 1.3 times faster with the error correction module turned on. Furthermore, it takes less than 4 minutes to process 280 GB of plain FASTQ sequencing data, while other applications take at least 22 minutes on a 48-core server when enabling the per-read over-representation analysis. C++ sources are available at https://github.com/RabbitBio/RabbitQCPlus.

Ecological momentary assessment of digital food and beverage marketing exposure and impact in young adults: A feasibility study.

Unhealthy food marketing is contributing to the obesity epidemic, but real-time insights into the mechanisms of this relationship are under-studied. Digital marketing is growing and following food and beverage (F&B) brands on social media is common, but measurement of exposure and impact of such marketing presents novel challenges. Thus, this study aimed to evaluate the feasibility of collecting data on exposure and impact of digital F&B marketing (DFM) using a smartphone-based ecological momentary assessment (EMA) methodology. We hypothesized that DFM-induced food cravings would vary based on whether (or not) participants engaged with F&B brands online. Participants were Singapore residents (n = 95, 21-40 years), recruited via telephone from an existing cohort. Participants were asked to upload screenshots of all sightings of online F&B marketing messages for seven days, and answer in-app contextual questions about sightings including whether any cravings were induced. Participants provided a total of 1310 uploads (median 9 per participant, Q1-Q3: 4-21) of F&B marketing messages, 27% of which were provided on Day 1, significantly more than on other days (P < 0.001). Followers of food/beverage brands on social media encountered 25.6 percentage points (95% CI 11.4, 39.7) more marketing messages that induced cravings than participants who were not followers. University education was also associated with more (18.1 percentage points; 95% CI 3.1, 33.1) encounters with marketing messages that induced cravings. It was practical and acceptable to participants to gather insights into digital F&B marketing exposure and impact using EMA in young adults, although a shorter study period is recommended in future studies. Followers of food and beverage brands on social media appear to be more prone to experience cravings after exposure to digital F&B marketing.

Flash-profilometry: fullfield lensless acquisition of spectral holograms for coherence scanning profilometry.

Flash-profilometry is a novel measurement approach based on the fullfield lensless acquisition of spectral holograms. It is based on spectral sampling of the mutual coherence function and the subsequent calculation of its propagation along the optical axis several times the depth-of-field. Numerical propagation of the entire coherence function, rather than solely the complex amplitude, allows to digitally reproduce a complete scanning white-light interferometric (WLI) measurement. Hence, the corresponding 3D surface profiling system presented here achieves precision in the low nanometer range along an axial measurement range of several hundred micrometers. Due to the lensless setup, it is compact, immune against dispersion effects and lightweight. Additionally, because of the spectral sampling approach, it is faster than conventional coherence scanning WLI and robust against mechanical distortions, such as vibrations and rigid body movements. Flash-profilometry is therefore suitable for a wide range of applications, such as surface metrology, optical inspection, and material science and appears to be particularly suitable for a direct integration into production environments.

Value of 68Ga-labeled bombesin antagonist (RM2) in the detection of primary prostate cancer comparing with [18F]fluoromethylcholine PET-CT and multiparametric MRI-a phase I/II study.

OBJECTIVES: The bombesin derivative RM2 is a GRPr antagonist with strong binding affinity to prostate cancer (PCa). In this study, the impact of [68Ga]Ga-RM2 positron emission tomography-computed tomography (PET-CT) for the detection of primary PCa was compared with that of [18F]FCH PET-CT and multiparametric magnetic resonance imaging (mpMRI). METHODS: This phase I/II study was conducted in 30 biopsy-positive PCa subjects. The patients were stratified into high (10 patients), intermediate (10 patients), and low risk (10 patients) for extraglandular metastases as defined by National Comprehensive Cancer Network (NCCN) criteria (NCCN Clinical Practice Guidelines in Oncology, 2016). The prostate gland was classified in 12 anatomic segments for data analysis of the imaging modalities as well as histopathologic findings. The segment with the highest radiotracer uptake was defined as the "index lesion." All cases were scheduled to undergo prostatectomy with pelvic lymph node (LN) dissection in intermediate- and high-risk patients. Intraprostatic and pelvic nodal [68Ga]Ga-RM2 and [18F]FCH PET-CT findings were correlated with mpMRI and histopathologic results. RESULTS: Of the 312 analyzed regions, 120 regions (4 to 8 lesions per patient) showed abnormal findings in the prostate gland. In a region-based analysis, overall sensitivity and specificity of [68Ga]Ga-RM2 PET-CT in the detection of primary tumor were 74% and 90%, respectively, while it was 60% and 80% for [18F]FCH PET-CT and 72% and 89% for mpMRI. Although the overall sensitivity of [68Ga]Ga-RM2 PET-CT was higher compared to that of [18F]FCH PET-CT and mpMRI, the statistical analysis showed only significant difference between [68Ga]Ga-RM2 PET-CT and [18F]FCH PET-CT in the intermediate-risk group (p = 0.01) and [68Ga]Ga-RM2 PET-CT and mpMRT in the high-risk group (p = 0.03). In the lesion-based analysis, there was no significant difference between SUVmax of [68Ga]Ga-RM2 and [18F]FCH PET-CT in the intraprostatic malignant lesions ([68Ga]Ga-RM2: mean SUVmax: 5.98 ± 4.13, median: 4.75; [18F]FCH: mean SUVmax: 6.08 ± 2.74, median: 5.5; p = 0.13). CONCLUSIONS: [68Ga]Ga-RM2 showed promising PET tracer for the detection of intraprostatic PCa in a cohort of patients with different risk stratifications. However, significant differences were only found between [68Ga]Ga-RM2 PET-CT and [18F]FCH PET-CT in the intermediate-risk group and [68Ga]Ga-RM2 PET-CT and mpMRT in the high-risk group. In addition, GRP-R-based imaging seems to play a complementary role to choline-based imaging for full characterization of PCa extent and biopsy guidance in low- and intermediate-metastatic-risk PCa patients and has the potential to discriminate them from those at higher risks. KEY POINTS: • [68Ga]Ga-RM2 is a promising PET tracer with a high detection rate for intraprostatic PCa especially in intermediate-risk prostate cancer patients. • GRPr-based imaging seems to play a complementary role to choline-based or PSMA-based PET/CT imaging in selected low- and intermediate-risk PCa patients for better characterization and eventually biopsy guidance of prostate cancer disease.

Results from the Singapore 2022 report card on physical activity for children and adolescents.

Background: While it has been established that physical activity (PA) is key to promote overall health and well-being, insufficient physical activity among children and adolescents is a global problem, including Singapore. It is important to understand the local PA landscape among children and adolescents to decrease surveillance gaps and identify areas for improvement in promoting PA. The present article provides an overview of the development of the 2022 Active Healthy Kids Singapore Report Card and the results, as well as underscore limitations and gaps in the available evidence related to PA among children and adolescents in Singapore. Methods: Following the Global Matrix 4.0, the available data between July 2010 to July 2020 was synthesized for all 10 indicators by the work group and reviewed by a panel of experts. Data sources included published scientific articles, government and non-government reports, national surveys, and unpublished data from on-going research studies. Where possible, grades were informed by nationally representative surveys or large-scale longitudinal studies. Results: The grades assigned were: Overall Physical Activity (C-), Organized Sport and Physical Activity (B-), Active Play (C-), Active Transportation (C), Sedentary Behaviours (C-), Physical Fitness (Incomplete), Family and Peers (C-), School (Incomplete), Community and Environment (A+), Government (B). Conclusion: This is the first comprehensive evaluation of PA among children and adolescents in Singapore. It provides baseline grades valuable for future comparison. It also illustrates gaps in the existing evidence which can inform future surveillance, facilitate international comparisons and enable global efforts in promoting physical activity.

Functional pixels: a pathway towards true holographic displays using today's display technology.

Today's 3D dynamic holographic display techniques suffer from severe limitations due to an available number of pixels that is several orders of magnitude lower than required by conventional approaches. We introduce a solution to this problem by introducing the concept of functional pixels. This concept is based on pixels that individually spatially modulate the amplitude and phase of incident light with a polynomial function, rather than just a constant phase or amplitude. We show that even in the simple case of a linear modulation of the phase, the pixel count can be drastically reduced up to 3 orders of magnitude while preserving most of the image details. This scheme can be easily implemented with already existing technology, such as micro mirror arrays that provide tip, tilt and piston movement. Even though the individual pixels need to be technologically more advanced, the comparably small number of such pixels required to form a display may pave the way towards true holographic dynamic 3D displays.

Rational discovery of molecular glue degraders via scalable chemical profiling.

Targeted protein degradation is a new therapeutic modality based on drugs that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. Of particular interest are molecular glues that can degrade otherwise unligandable proteins by orchestrating direct interactions between target and ligase. However, their discovery has so far been serendipitous, thus hampering broad translational efforts. Here, we describe a scalable strategy toward glue degrader discovery that is based on chemical screening in hyponeddylated cells coupled to a multi-omics target deconvolution campaign. This approach led us to identify compounds that induce ubiquitination and degradation of cyclin K by prompting an interaction of CDK12-cyclin K with a CRL4B ligase complex. Notably, this interaction is independent of a dedicated substrate receptor, thus functionally segregating this mechanism from all described degraders. Collectively, our data outline a versatile and broadly applicable strategy to identify degraders with nonobvious mechanisms and thus empower future drug discovery efforts.

Comparison of individual and common wavelength-operation for 785 nm Y-branch DBR ridge waveguide diode lasers with adjustable spectral distance.

An experimental comparison between individual and common wavelength-operation of a Y-branch distributed Bragg reflector (DBR) ridge waveguide (RW) laser at 785 nm with an electrically adjustable spectral distance is presented. The dual-wavelength Y-branch laser combines two laser cavities via a Y-section to a common output section. DBR gratings with different grating periods are associated with the two cavities, which set the emission wavelengths of the two branches. Implemented resistive heater elements allow separate wavelength tuning of the two branches, which can be operated individually for alternating emission wavelengths in applications such as differential absorption spectroscopy or shifted excitation Raman difference spectroscopy. Common wavelength operation simultaneously generates two emission lines suitable for the generation of THz radiation using difference frequency mixing. Hereby, the devices could potentially be used as single-chip light sources for a combination of Raman and THz applications. For the wavelength-operation comparison presented, the devices were operated up to optical output powers of about 105 and 185 mW in individual and common wavelength-operation mode, respectively. In individual operation mode, the devices show spectral single-mode emission over the whole operation range. In common operation mode, the spectral emission is predominantly single mode up to an optical output power of 65 mW. In both operation modes, mode hops typical for DBR lasers occur. At an optical output power of 50 mW, tuning of the spectral distance between the two wavelengths using the implemented resistor heaters is demonstrated. In both modes of wavelength operation, a flexible frequency difference between 0 and 0.8 THz (0 and 1.6 nm) with predominantly single-mode spectral emission is obtained.

10% Body weight (gain) change as criterion for the maximum tolerated dose: A critical analysis.

The concept of the Maximum Tolerated Dose (MTD) was introduced in the seventies for carcinogenicity testing and was defined as the highest dose inducing clear toxicity, but not mortality by causes other than cancer. As estimation of the MTD in a carcinogenicity study, the highest dose that causes a 10% decrease in body weight compared to control animals over the course of a 90-day study, was formulated as a suitable criterion. This criterion was not seen as indicator of excessive toxicity but as a means to avoid false negative outcomes in a carcinogenicity study, as tumor formation may be reduced when body weight is significantly decreased. The body weight-based MTD criterion, however, turned up in carcinogenicity test guidelines and guidance (e.g., from OECD) as the highest dose that causes a 10% decrease in body weight gain relative to controls. Moreover, the 10% decrease in body weight gain criterion for MTD also ended up in test guidelines and guidances for toxicity endpoints other than carcinogenicity, so outside the context it was intended for. A 10% decrease in body weight gain relative to controls is however not a biologically relevant effect as it corresponds to less than 3% body weight reduction relative to controls in a 90-day study, which is within the normal variation in body weight. It therefore should certainly not be considered as a condition of excessive toxicity. Using the 10% lower weight gain criterion and incorrectly associating it with excessive toxicity has major implications for top dose selection in regulatory safety studies, resulting in tests performed at doses too low to elicit toxicity. This negatively impacts the reliability of studies and their regulatory usability; moreover, it results in a waste of experimental animals, which is ethically highly undesirable. Hence, our plea is to remove this MTD criterion for top dose selection in test guidelines and guidances for toxicity endpoints other than carcinogenicity and to reinstall the original 10% decrease in body weight criterion in test guidelines and guidances for carcinogenicity.

Occupational sitting time, its determinants and intervention strategies in Malaysian office workers: a mixed-methods study.

Adults who accumulate a lot of sedentary time per day are at an increased risk of metabolic syndrome, type 2 diabetes, and hypertension. Prolonged sitting is also associated with depression, anxiety, bipolar disorder and schizophrenia. With the increase in desk-based office work, many office workers spend long hours sitting at the workplace. The aim of this study was to assess occupational sitting time in Malaysian government office workers, and investigate determinants of occupational sitting time and potential strategies to interrupt sitting time. We conducted a mixed-methods study consisting of a survey and focus group discussions (FGDs). A total of 1338 office workers from 24 Malaysian ministries completed the Occupational Sitting and Physical Activity Questionnaire. Twenty-nine office workers who spent at least 7 h per day sitting at work participated in FGDs. We enquired about knowledge, awareness and perceptions related to prolonged sitting time, barriers and facilitators to sitting time at work, and potential intervention strategies. Mean daily sitting time at work was 5.96 h (standard deviation = 1.37 h). FDGs confirmed barriers and facilitators to sitting time in accordance with the social-ecological model for health. Intrapersonal, social and physical environmental factors as well as organizational culture and organizational policy were mentioned to affect occupational sitting time. The results show that Malaysian government office workers spent a significant amount of time sitting at work and we identified multi-level factors influencing sitting time. A smartphone-based intervention to interrupt sitting time at work was suggested and is currently being tested.

Sedentary behavior is associated with adverse health outcomes including non-communicable diseases and mental disorders. With the increase in desk-based office work, many office workers spend long hours sitting at the workplace. Our study assessed occupational sitting time in Malaysian government office workers, and investigated determinants of occupational sitting time and potential strategies to interrupt sitting time. We conducted a survey and focus group discussions (FGDs). A total of 1338 office workers completed the Occupational Sitting and Physical Activity Questionnaire. Twenty-nine office workers who spent at least 7 h per day sitting at work participated in FGDs. We enquired about knowledge, awareness and perceptions related to prolonged sitting time, barriers and facilitators to sitting time at work, and potential intervention strategies. The mean daily sitting time at work was 5.96 h (standard deviation = 1.37 h). FGD participants mentioned that intrapersonal, social and physical environmental factors as well as organizational culture and organizational policy affected occupational sitting time. They suggested a smartphone-based intervention to interrupt sitting time at work.

When e-learning takes centre stage amid COVID-19: Dental educators' perspectives and their future impacts.

INTRODUCTION: The COVID-19 pandemic has necessitated an unprecedented shift from face-to-face teaching to e-learning. Previous surveys revealed the negative impact of COVID-19 on dental education and the physical and psychological well-being of dental students. This qualitative study aimed to investigate the perspectives of dental educators towards e-learning during the pandemic and the impact of this experience on their future adoption of e-learning. MATERIALS AND METHODS: Semi-structured interviews with dental educators from the National University of Singapore were conducted over Zoom. Audio recordings were transcribed verbatim and subjected to thematic analysis. Data saturation was reached. Consolidated criteria for reporting qualitative research (COREQ) was followed. RESULTS: Fifteen out of 22 (68%) eligible dental educators were interviewed. Educators had minimal prior e-learning experience. They encountered difficulties in engaging students, assessing students' understanding and adapting their teaching. A practical challenge was to ensure the well-rounded training of competent dentists with adequate patient-interaction skills through e-learning. Self-motivation of the audience, class size, type of teaching and complexity of the material were perceived as factors influencing the suitability of the e-learning format. Educators reported an increased confidence after this emergency e-learning experience. Some considered sustaining or expanding e-learning in their future teaching practice and highlighted the need for continued investment and institutional support, training on the pedagogy of e-learning modalities and curriculum redesign to accommodate blended learning approaches. CONCLUSIONS: Although the shift to e-learning during the COVID-19 pandemic presented a myriad of challenges, dental educators gained experience and confidence which may accelerate the pace of future e-learning adoption and innovation.

24-Norursodeoxycholic acid reshapes immunometabolism in CD8+ T cells and alleviates hepatic inflammation.

BACKGROUND & AIMS: 24-Norursodeoxycholic acid (NorUDCA) is a novel therapeutic bile acid used to treat immune-mediated cholestatic liver diseases, such as primary sclerosing cholangitis (PSC), where dysregulated T cells including CD8+ T cells contribute to hepatobiliary immunopathology. We hypothesized that NorUDCA may directly modulate CD8+ T cell function thus contributing to its therapeutic efficacy. METHODS: NorUDCA's immunomodulatory effects were first studied in Mdr2-/- mice, as a cholestatic model of PSC. To differentiate NorUDCA's immunomodulatory effects on CD8+ T cell function from its anticholestatic actions, we also used a non-cholestatic model of hepatic injury induced by an excessive CD8+ T cell immune response upon acute non-cytolytic lymphocytic choriomeningitis virus (LCMV) infection. Studies included molecular and biochemical approaches, flow cytometry and metabolic assays in murine CD8+ T cells in vitro. Mass spectrometry was used to identify potential CD8+ T cell targets modulated by NorUDCA. The signaling effects of NorUDCA observed in murine cells were validated in circulating T cells from patients with PSC. RESULTS: NorUDCA demonstrated immunomodulatory effects by reducing hepatic innate and adaptive immune cells, including CD8+ T cells in the Mdr2-/- model. In the non-cholestatic model of CD8+ T cell-driven immunopathology induced by acute LCMV infection, NorUDCA ameliorated hepatic injury and systemic inflammation. Mechanistically, NorUDCA demonstrated strong immunomodulatory efficacy in CD8+ T cells affecting lymphoblastogenesis, expansion, glycolysis and mTORC1 signaling. Mass spectrometry identified that NorUDCA regulates CD8+ T cells by targeting mTORC1. NorUDCA's impact on mTORC1 signaling was further confirmed in circulating PSC CD8+ T cells. CONCLUSIONS: NorUDCA has a direct modulatory impact on CD8+ T cells and attenuates excessive CD8+ T cell-driven hepatic immunopathology. These findings are relevant for treatment of immune-mediated liver diseases such as PSC. LAY SUMMARY: Elucidating the mechanisms by which 24-norursodeoxycholic acid (NorUDCA) works for the treatment of immune-mediated liver diseases, such as primary sclerosing cholangitis, is of considerable clinical interest. Herein, we uncovered an unrecognized property of NorUDCA in the immunometabolic regulation of CD8+ T cells, which has therapeutic relevance for immune-mediated liver diseases, including PSC.

An illuminated respiratory activity monitoring system identifies priming-active compounds in plant seedlings.

BACKGROUND: Growing large crop monocultures and heavily using pesticides enhances the evolution of pesticide-insensitive pests and pathogens. To reduce pesticide use in crop cultivation, the application of priming-active compounds (PrimACs) is a welcome alternative. PrimACs strengthen the plant immune system and could thus help to protect plants with lower amounts of pesticides. PrimACs can be identified, for example, by their capacity to enhance the respiratory activity of parsley cells in culture as determined by the oxygen transfer rate (OTR) using the respiration activity monitoring system (RAMOS) or its miniaturized version, µRAMOS. The latter was designed for with suspensions of bacteria and yeast cells in microtiter plates (MTPs). So far, RAMOS or µRAMOS have not been applied to adult plants or seedlings, which would overcome the limitation of (µ)RAMOS to plant suspension cell cultures. RESULTS: In this work, we introduce a modified µRAMOS for analysis of plant seedlings. The novel device allows illuminating the seedlings and records the respiratory activity in each well of a 48-well MTP. To validate the suitability of the setup for identifying novel PrimAC in Arabidopsis thaliana, seedlings were grown in MTP for seven days and treated with the known PrimAC salicylic acid (SA; positive control) and the PrimAC candidate methyl 1-(3,4-dihydroxyphenyl)-2-oxocyclopentane-1-carboxylate (Tyr020). Twenty-eight h after treatment, the seedlings were elicited with flg22, a 22-amino acid peptide of bacterial flagellin. Upon elicitation, the respiratory activity was monitored. The evaluation of the OTR course reveals Tyr020 as a likely PrimAC. The priming-inducing activity of Tyr020 was confirmed using molecular biological analyses in A. thaliana seedlings. CONCLUSION: We disclose the suitability of µRAMOS for identifying PrimACs in plant seedlings. The difference in OTR during a night period between primed and unprimed plants was distinguishable after elicitation with flg22. Thus, it has been shown that the µRAMOS device can be used for a reliable screening for PrimACs in plant seedlings.

Γ-profilometry: a new paradigm for precise optical metrology.

We show that the shape of a surface can be unambiguously determined from investigating the coherence function of a wave-field reflected by the surface and without the requirement of a reference wave. Spatio-temporal sampling facilitates the identification of temporal shifts of the coherence function that correspond to finite height differences of the surface. Evaluating these finite differences allows for the reconstruction of the surface using a numerical integration procedure. Spatial sampling of the coherence function is provided by a shear interferometer whereas temporal sampling is achieved by means of a Soleil-Babinet compensator. This low coherence profiling method allows to determine the shape of an object with sub-micrometer resolution and over a large unambiguity range, although it does not require any isolation against mechanical vibration. The approach therefore opens up a new avenue for precise, rugged optical metrology suitable for industrial in-line applications.

The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis.

The maize smut fungus Ustilago maydis is a model organism for elucidating host colonization strategies of biotrophic fungi. Here, we performed an in depth transcriptional profiling of the entire plant-associated development of U. maydis wild-type strains. In our analysis, we focused on fungal metabolism, nutritional strategies, secreted effectors, and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to stages on the plant surface, establishment of biotrophy, and induction of tumors. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen assimilation are important virulence factors. By measuring the intramodular connectivity of transcription factors, we identified the potential drivers for the virulence modules. While known components of the b-mating type cascade emerged as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role for leaf tumor formation and effector gene expression for one of these transcription factors.

783 nm wavelength stabilized DBR tapered diode lasers with a 7 W output power.

Wavelength stabilized distributed Bragg reflector (DBR) tapered diode lasers at 783 nm will be presented. The devices are based on GaAsP single quantum wells embedded in a large optical cavity leading to a vertical far field angle of about 29° (full width at half maximum). The 3-inch (7.62 cm) wafers are grown using metalorganic vapor phase epitaxy. In a full wafer process, 4 mm long DBR tapered lasers are manufactured. The devices consist of a 500 µm long 10th order surface DBR grating that acts as rear side mirror. After that, a 1 mm long ridge waveguide section is realized for lateral confinement, which is connected to a 2.5 mm long flared section having a full taper angle of 6°. At an injection current of 8 A, a maximum output power of about 7 W is measured. At output powers up to 6 W, the measured emission width limited by the resolution of the spectrometer is smaller than 19 pm. Measured at 1/e2 level at this output power, the lateral beam waist width is 11.5 µm, the lateral far field angle 12.5°, and the lateral beam parameter M2 2.5. The respective parameters measured using the second moments are 31 µm, 15.2°, and 8.3. 70% of the emitted power is originated from the central lobe.

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads.

BACKGROUND: Obtaining data from single-cell transcriptomic sequencing allows for the investigation of cell-specific gene expression patterns, which could not be addressed a few years ago. With the advancement of droplet-based protocols the number of studied cells continues to increase rapidly. This establishes the need for software tools for efficient processing of the produced large-scale datasets. We address this need by presenting RainDrop for fast gene-cell count matrix computation from single-cell RNA-seq data produced by 10x Genomics Chromium technology. RESULTS: RainDrop can process single-cell transcriptomic datasets consisting of 784 million reads sequenced from around 8.000 cells in less than 40 minutes on a standard workstation. It significantly outperforms the established Cell Ranger pipeline and the recently introduced Alevin tool in terms of runtime by a maximal (average) speedup of 30.4 (22.6) and 3.5 (2.4), respectively, while keeping high agreements of the generated results. CONCLUSIONS: RainDrop is a software tool for highly efficient processing of large-scale droplet-based single-cell RNA-seq datasets on standard workstations written in C++. It is available at https://gitlab.rlp.net/stnieble/raindrop .

A big data approach to metagenomics for all-food-sequencing.

BACKGROUND: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoids some of the shortcomings of targeted PCR-based methods, it requires the comparison of sequence reads to large collections of reference genomes. The steadily increasing amount of available reference genomes establishes the need for efficient big data approaches. RESULTS: We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters. It is orders-of-magnitude faster than our previous alignment-based AFS pipeline. In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy. Furthermore, the usage of an efficient database partitioning scheme allows for the processing of massive collections of reference genomes with reduced memory requirements on a workstation (AFS-MetaCache) or on a Spark-based compute cluster (MetaCacheSpark). CONCLUSIONS: We present a fast yet accurate screening method for whole genome shotgun sequencing-based biosurveillance applications such as food testing. By relying on a big data approach it can scale efficiently towards large-scale collections of complex eukaryotic and bacterial reference genomes. AFS-MetaCache and MetaCacheSpark are suitable tools for broad-scale metagenomic screening applications. They are available at https://muellan.github.io/metacache/afs.html (C++ version for a workstation) and https://github.com/jmabuin/MetaCacheSpark (Spark version for big data clusters).