Alternative dimethylsulfoniopropionate biosynthesis enzymes in diverse and abundant microorganisms.

Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound with roles in stress protection, chemotaxis, nutrient and sulfur cycling and climate regulation. Here we report the discovery of a bifunctional DMSP biosynthesis enzyme, DsyGD, in the transamination pathway of the rhizobacterium Gynuella sunshinyii and some filamentous cyanobacteria not previously known to produce DMSP. DsyGD produces DMSP through its N-terminal DsyG methylthiohydroxybutyrate S-methyltransferase and C-terminal DsyD dimethylsulfoniohydroxybutyrate decarboxylase domains. Phylogenetically distinct DsyG-like proteins, termed DSYE, with methylthiohydroxybutyrate S-methyltransferase activity were found in diverse and environmentally abundant algae, comprising a mix of low, high and previously unknown DMSP producers. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, were globally more abundant DMSP producers than those with previously described DMSP synthesis genes. This work greatly increases the number and diversity of predicted DMSP-producing organisms and highlights the importance of Pelagophyceae and other DSYE-containing algae in global DMSP production and sulfur cycling.

Photostasis and photosynthetic adaptation to polar life.

Photostasis is the light-dependent maintenance of energy balance associated with cellular homeostasis in photoautotrophs. We review evidence that illustrates how photosynthetic adaptation in polar photoautrophs such as aquatic green algae, cyanobacteria, boreal conifers as well as terrestrial angiosperms exhibit an astonishing plasticity in structure and function of the photosynthetic apparatus. This plasticity contributes to the maintenance of photostasis, which is essential for the long-term survival in the seemingly inhospitable Antarctic and Arctic habitats. However, evidence indicates that polar photoautrophic species exhibit different functional solutions for the maintenance of photostasis. We suggest that this reflects, in part, the genetic diversity symbolized by inherent genetic redundancy characteristic of polar photoautotrophs which enhances their survival in a thermodynamically challenging environment.

Occupancy of the HbYX hydrophobic pocket is sufficient to induce gate opening in the archaeal 20S proteasomes.

Enhancing proteasome function has been a long-standing but challenging target of interest for the potential treatment of neurodegenerative diseases, emphasizing the importance of understanding proteasome activation mechanisms. Most proteasome activator complexes use the C-terminal HbYX motif to bind and trigger gate-opening in the 20S proteasome. This study defines a critical molecular interaction in the HbYX mechanism that triggers gate opening. Here, we focus on the Hb site interaction and find it plays a surprisingly central and crucial role in driving the allosteric conformational changes that induce gate opening in the archaeal 20S. We examined the cryo-EM structure of two mutant archaeal proteasomes, αV24Y T20S and αV24F T20S. These two mutants were engineered to place a bulky aromatic residue in the HbYX hydrophobic pocket and both mutants are highly active, though their mechanisms of activation are undefined. Collectively, our findings indicate that the interaction between the Hb group of the HbYX motif and its corresponding hydrophobic pocket is sufficient to induce gate opening in a mechanistically similar way to the HbYX motif. The involved activation mechanism appears to involve expansion of this hydrophobic binding site affecting the state of the IT switch to triggering gate-opening. Furthermore, we show that the canonical αK66 residue, understood to be critical for proteasome activator binding, plays a key role in stabilizing the open gate, irrespective of activator binding. This study differentiates between the residues in the HbYX motif that support binding interactions ("YX") versus those that allosterically contribute to gate opening (Hb). The insights reported here will guide future drug development efforts, particularly in designing small molecule proteasome activators, by targeting the identified hydrophobic pocket.

Single-cell transcriptomics reveal synergistic and antagonistic effects of T21 and GATA1s on hematopoiesis.

Trisomy 21 (T21), or Down syndrome (DS), is associated with baseline macrocytic erythrocytosis, thrombocytopenia, and neutrophilia, and transient abnormal myelopoiesis (TAM) and myeloid leukemia of DS (ML-DS). TAM and ML-DS blasts both arise from an aberrant megakaryocyte-erythroid progenitor and exclusively express GATA1s, the truncated isoform of GATA1 , while germline GATA1s mutations in a non-T21 context lead to congenital cytopenias without a leukemic predisposition. This suggests that T21 and GATA1s perturb hematopoiesis independently and synergistically, but this interaction has been challenging to study in part due to limited human cell and murine models. To dissect the developmental impacts of GATA1s on hematopoiesis in euploid and T21 cells, we performed a single-cell RNA-sequencing timecourse on hematopoietic progenitors (HPCs) derived from isogenic human induced pluripotent stem cells differing only by chromosome 21 and/or GATA1 status. These HPCs were surprisingly heterogeneous and displayed spontaneous lineage skew apparently dictated by T21 and/or GATA1s. In euploid cells, GATA1s nearly eliminated erythropoiesis, impaired MK maturation, and promoted an immature myelopoiesis, while in T21 cells, GATA1s appeared to compete with the enhanced erythropoiesis and suppressed megakaryopoiesis driven by T21 to give rise to immature erythrocytes, MKs, and myeloid cells. T21 and GATA1s both disrupted temporal regulation of lineage-specific transcriptional programs and specifically perturbed cell cycle genes. These findings in an isogenic system can thus be attributed specifically to T21 and GATA1s and suggest that these genetic changes together enhance HPC proliferation at the expense of maturation, consistent with a pro-leukemic phenotype.

Long-read RNA sequencing can probe organelle genome pervasive transcription.

40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.

A toolbox to engineer the highly productive cyanobacterium Synechococcus sp. PCC 11901.

Synechococcus sp. PCC 11901 (PCC 11901) is a fast-growing marine cyanobacterial strain that has a capacity for sustained biomass accumulation to very high cell densities, comparable to that achieved by commercially relevant heterotrophic organisms. However, genetic tools to engineer PCC 11901 for biotechnology applications are limited. Here we describe a suite of tools based on the CyanoGate MoClo system to unlock the engineering potential of PCC 11901. First, we characterised neutral sites suitable for stable genomic integration that do not affect growth even at high cell densities. Second, we tested a suite of constitutive promoters, terminators, and inducible promoters including a 2,4-diacetylphloroglucinol (DAPG)-inducible PhlF repressor system, which has not previously been demonstrated in cyanobacteria, and showed tight regulation and a 228-fold dynamic range of induction. Lastly, we developed a DAPG-inducible dCas9-based CRISPR interference (CRISPRi) system and a modular method to generate markerless mutants using CRISPR-Cas12a. Based on our findings, PCC 11901 is highly responsive to CRISPRi-based repression and showed high efficiencies for single insertion (31-81%) and multiplex double insertion (25%) genome editing with Cas12a. We envision that these tools will lay the foundations for the adoption of PCC 11901 as a robust model strain for engineering biology and green biotechnology.

Protein Intake and Physical Activity Levels as Determinants of Sarcopenia Risk in Community-Dwelling Older Adults.

Community screening for sarcopenia is complex, with barriers including access to specialized equipment and trained staff to conduct body composition, strength and function assessment. In the current study, self-reported dietary protein intake and physical activity (PA) in adults ≥65 years was assessed relative to sarcopenia risk, as determined by body composition, strength and physical function assessments, consistent with the European Working Group on Sarcopenia in Older People (EWGSOP) definition. Of those screened (n = 632), 92 participants (77% female) were assessed as being at high risk of developing sarcopenia on the basis of dietary protein intake ≤1 g∙kg-1∙day-1 [0.9 (0.7-0.9) g∙kg-1∙day-1] and moderate intensity physical activity <150 min.week-1. A further 31 participants (65% female) were defined as being at low risk, with both protein intake [1.2 (1.1-1.5) g∙kg-1∙day-1] and PA greater than the cut-off values. High-risk participants had reduced % lean mass [53.5 (7.8)% versus 54.8 (6.1)%, p < 0.001] and impaired strength and physical function. Notably, high-risk females exhibited greater deficits in lean mass and strength, with minimal differences between groups for males. In community-dwelling older adults, self-reported low protein intake and low weekly PA is associated with heightened risk for sarcopenia, particularly in older women. Future research should determine whether early intervention in older adults with low protein intake and PA attenuates functional decline.

A comparison of hippocampal and retrosplenial cortical spatial and contextual firing patterns.

The hippocampus (HPC) and retrosplenial cortex (RSC) are key components of the brain's memory and navigation systems. Lesions of either region produce profound deficits in spatial cognition and HPC neurons exhibit well-known spatial firing patterns (place fields). Recent studies have also identified an array of navigation-related firing patterns in the RSC. However, there has been little work comparing the response properties and information coding mechanisms of these two brain regions. In the present study, we examined the firing patterns of HPC and RSC neurons in two tasks which are commonly used to study spatial cognition in rodents, open field foraging with an environmental context manipulation and continuous T-maze alternation. We found striking similarities in the kinds of spatial and contextual information encoded by these two brain regions. Neurons in both regions carried information about the rat's current spatial location, trajectories and goal locations, and both regions reliably differentiated the contexts. However, we also found several key differences. For example, information about head direction was a prominent component of RSC representations but was only weakly encoded in the HPC. The two regions also used different coding schemes, even when they encoded the same kind of information. As expected, the HPC employed a sparse coding scheme characterized by compact, high contrast place fields, and information about spatial location was the dominant component of HPC representations. RSC firing patterns were more consistent with a distributed coding scheme. Instead of compact place fields, RSC neurons exhibited broad, but reliable, spatial and directional tuning, and they typically carried information about multiple navigational variables. The observed similarities highlight the closely related functions of the HPC and RSC, whereas the differences in information types and coding schemes suggest that these two regions likely make somewhat different contributions to spatial cognition.

Eco-climate drivers shape virome diversity in a globally invasive tick species.

Spillovers of viruses into human occur more frequently under warmer conditions, particularly arboviruses. The invasive tick species Haemaphysalis longicornis poses a significant public health threat due to its global expansion and its potential to carry a wide range of pathogens. We analyzed meta-transcriptomic data from 3595 adult H. longicornis ticks collected between 2016 and 2019 in 22 provinces across China, encompassing diverse ecological conditions. Generalized additive modelling revealed that climate factors exerted a stronger influence on the virome of H. longicornis compared to other ecological factors, such as ecotypes, distance to coastline, animal host, tick gender, and anti-viral immunity. We investigated the mechanistic understanding of how climate changes drive the tick virome using causality inference and emphasized its significance for public health. Our findings demonstrated that higher temperatures and lower relative humidity/precipitation contribute to variations in animal host diversity, leading to an increased diversity of tick virome, particularly the evenness of vertebrate associated viruses. This finding may explain the evolution of tick-borne viruses into generalists across multiple hosts, thereby increasing the probability of spillover events involving tick-borne pathogens. Deep learning projections indicate that the diversity of H. longicornis virome is expected to increase in 81.9% of regions under the SSP8.5 scenario from 2019-2030. Extension of surveillance should be implemented to avert the spread of tick-borne diseases.

Leaflet modification before transcatheter aortic valve implantation in patients at risk for coronary obstruction: the ShortCut study.

BACKGROUND AND AIMS: This trial sought to assess the safety and efficacy of ShortCut, the first dedicated leaflet modification device, prior to transcatheter aortic valve implantation (TAVI) in patients at risk for coronary artery obstruction. METHODS: This pivotal prospective study enrolled patients with failed bioprosthetic aortic valves scheduled to undergo TAVI and were at risk for coronary artery obstruction. The primary safety endpoint was procedure-related mortality or stroke at discharge or 7 days, and the primary efficacy endpoint was per-patient leaflet splitting success. Independent angiographic, echocardiographic, and computed tomography core laboratories assessed all images. Safety events were adjudicated by a clinical events committee and data safety monitoring board. RESULTS: Sixty eligible patients were treated (77.0 ± 9.6 years, 70% female, 96.7% failed surgical bioprosthetic valves, 63.3% single splitting and 36.7% dual splitting) at 22 clinical sites. Successful leaflet splitting was achieved in all (100%; 95% confidence interval [CI] 94-100.0%, p<0.001) patients. Procedure time, including imaging confirmation of leaflet splitting, was 30.6 ± 17.9 min. Freedom from the primary safety endpoint was achieved in 59 (98.3%; 95% CI [91.1-100%]) patients, with no mortality and one (1.7%) disabling stroke. At 30 days, freedom from coronary obstruction was 95% (95% CI 86.1-99.0%). Within 90 days, freedom from mortality was 95% (95% CI 86.1-99.0%]), without any cardiovascular deaths. CONCLUSIONS: Modification of failed bioprosthetic aortic valve leaflets using ShortCut was safe, achieved successful leaflet splitting in all patients, and was associated with favorable clinical outcomes in patients at risk for coronary obstruction undergoing TAVI.

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences.

BACKGROUND: Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS: In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS: ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.

Percutaneous coronary intervention for bifurcation coronary lesions using optimised angiographic guidance: the 18th consensus document from the European Bifurcation Club.

The 2023 European Bifurcation Club (EBC) meeting took place in Warsaw in October, and the latest evidence for the use of intravascular ultrasound (IVUS) and optical coherence tomography (OCT) to optimise percutaneous coronary interventions (PCI) on coronary bifurcation lesions (CBLs) was a major focus. The topic generated deep discussions and general appraisal on the potential benefits of IVUS and OCT in PCI procedures. Nevertheless, despite an increasing recognition of IVUS and OCT capabilities and their recognised central role for guidance in complex CBL and left main PCI, it is expected that angiography will continue to be the primary guidance modality for CBL PCI, principally due to educational and economic barriers. Mindful of the restricted access/adoption of intracoronary imaging for CBL PCI, the EBC board decided to review and describe a series of tips and tricks which can help to optimise angiography-guided PCI for CBLs. The identified key points for achieving an optimal angiography-guided PCI include a thorough analysis of pre-PCI images (computed tomography angiography, multiple angiographic views, quantitative coronary angiography vessel estimation), a systematic application of the technical steps suggested for a given selected technique, an intraprocedural or post-PCI use of stent enhancement and a low threshold for bailout use of intravascular imaging.

Sociodemographic predictors of perceived weight discrimination.

BACKGROUND: Perceived weight discrimination is associated with increased risk for chronic diseases and reduced life expectancy. Nevertheless, little is known about perceived weight discrimination in racial, ethnic, and sexual minority groups or in individuals at the intersections of those groups. The goal of this study was to identify sociodemographic predictors of perceived weight discrimination. SUBJECTS/METHODS: A diverse sample of adults (37% Black/African American, 36% Latino, 29% sexual minority) with a body mass index (BMI) ≥ 18.5 kg/m2 were recruited from a national US panel to complete an online survey (N = 2454). Perceived weight discrimination was assessed with the Stigmatizing Situations Survey-Brief (SSI-B). Using hierarchical linear regression analysis, SSI-B scores were predicted from the four sociodemographic characteristics of interest (gender, race, ethnicity, and sexual orientation) while controlling for BMI, age, education, and income (Step 1). At Step 2, all two-way interactions between the four sociodemographic characteristics were added to the model. RESULTS: At Step 1, higher SSI-B scores were observed for Latino (vs. non-Latino) adults, sexual minority (vs. heterosexual) adults, younger (vs. older) adults, adults with higher (vs. lower) levels of education, and adults with higher (vs. lower) BMI. At Step 2, race interacted with gender, ethnicity, and sexual orientation to predict SSI-B scores such that relatively higher scores were observed for non-Black women, Black men, adults who identified as Black and Latino, and non-Black sexual minority adults. CONCLUSIONS: Perceived weight discrimination varied across sociodemographic groups, with some subgroups reporting relatively high frequency. Black race appeared to be protective for some subgroups (e.g., Black women), but risk-enhancing for others (e.g., Black men, individuals who identified as Black and Latino). Additional research is needed to identify specific factors that cause certain sociodemographic groups -and indeed, certain individuals-to perceive higher levels of weight discrimination than others.

Delayed development of spinal stenosis at the spinal cord stimulator percutaneous lead entry point: case report and literature review.

BACKGROUND: Spinal cord stimulation (SCS) is an efficacious treatment for various refractory chronic pain syndromes. Serious complications including spinal cord compression (SCC) are rare with 19 previous reports which are mainly attributed to fibrotic scar tissue formation at the distal end of the leads at the location of the contacts. We report a case of SCC following SCS implantation at the lead entry location secondary to a delayed progression of spinal canal stenosis. CASE PRESENTATION: A patient in her early 70s underwent SCS implantation with adequate therapeutic benefit for approximately 2 years before citing complaints of increasing lower back pain and lower extremity radicular pain. Lumbar spine X-rays excluded lead migration as a causative factor. An MRI of the lumbar spine obtained 30 months following SCS implantation demonstrated a marked interval progression of central canal stenosis secondary to facet and ligamentous hypertrophy manifesting in compression of the spinal cord at the lead entry location. An L1-L2 decompressive laminectomy with hardware removal resulted in the resolution of her symptoms. A literature search conducted with the PubMed database identified previously published cases of SCC following SCS implantation which highlighted the rarity of this complication. CONCLUSION: Our case report urges physicians of SCS patients, noting a loss of therapeutic benefit with their device, to investigate new pathologies including SCC. Furthermore, our case highlights clinical symptoms and surgical treatments of SCC. Paddle leads are more commonly implicated in published cases of SCC than percutaneous leads. Lastly, MRI conditionality is critical to identifying cases of SCC.

Impact of commissural versus coronary alignment on risk of coronary obstruction following transcatheter aortic valve implantation.

Transcatheter aortic valve implantation (TAVI) with commissural alignment aims to limit the risk of coronary occlusion and maintain good coronary access. However, due to coronary origin eccentricity within the coronary cusp, coronary-commissural overlap (CCO) may still occur. TAVI using coronary alignment, rather than commissural alignment, may further improve coronary access. To compare rates of CCO after TAVI using commissural versus coronary alignment methodology. Cardiac CT scans from 102 patients with severe (tricuspid) aortic stenosis referred for TAVI were analysed. Native cusp asymmetry and coronary eccentricity were defined and used to simulate TAVI using commissural versus coronary alignment. Rates of optimal coronary alignment (< 10° from cusp centre) and severe misalignment (< 15° from coronary-commissural overlap) were compared. Additionally, the impact of valve misalignment during implantation was assessed. The native right coronary artery (RCA) origin was 15.8° (9.5 to 24°) closer to the right coronary cusp/non-coronary cusp (RCC-NCC) commissure than the centre of the right coronary cusp. The native left coronary artery (LCA) origin was 4.5° (0 to 11.5°) closer to the left coronary cusp/non-coronary cusp (LCC-NCC) commissure than the centre of the left coronary cusp (p < 0.01). Compared to commissural alignment, coronary alignment doubled the proportion of optimally-aligned RCAs (62/102 [60.8%] vs. 31/102 [30.4%]; p < 0.001), without a significant change in optimal LCA alignment (62/102 [60.8% vs. 74/102 [72.6%]; p = 0.07). There were no cases of severe misalignment with either strategy. Simulating 15° of valve misalignment resulted in severe RCA compromise risk in 7/102 (6.9%) of commissural alignment cases, compared to none using coronary alignment. Fluoroscopic projection was similar with both approaches. Coronary alignment resulted in a 2-fold increase of optimal TAVI positioning relative to the RCA ostium when compared to commissural alignment without impacting the LCA. Use of coronary alignment rather than commissural alignment may improve coronary access after TAVI and is less sensitive to valve rotational error, particularly for the right coronary artery.

Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.

Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis.

Correction: Limitations of rapid diagnostic tests in malaria surveys in areas with varied transmission intensity in Uganda 2017-2019: Implications for selection and use of HRP2 RDTs.

[This corrects the article DOI: 10.1371/journal.pone.0244457.].