Nanopore and Illumina sequencing reveal different viral populations from human gut samples.

The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.

Induced Burkholderia prophages detected from the hemoculture: a biomarker for Burkholderia pseudomallei infection.

Bacteriophages (phages), viruses that infect bacteria, are found in abundance not only in the environment but also in the human body. The use of phages for the diagnosis of melioidosis, a tropical infectious disease caused by Burkholderia pseudomallei, is emerging as a promising novel approach, but our understanding of conditions under which Burkholderia prophages can be induced remains limited. Here, we first demonstrated the isolation of Burkholderia phages from the hemocultures of melioidosis patients. The B. pseudomallei-positive hemoculture bottles were filtered to remove bacteria, and then phages were isolated and purified by spot and double agar overlay plaque assays. Forty blood samples (hemoculture-confirmed melioidosis) were tested, and phages were found in 30% of the samples. Transmission electron microscopy and genome analysis of the isolated phages, vB_HM387 and vB_HM795, showed that both phages are Myoviruses. These two phages were stable at a pH of 5-7 and temperatures of 25-37°C, suggesting their ability to survive in human blood. The genome sizes of vB_HM387 and vB_HM795 are 36.3 and 44.0 kb, respectively. A phylogenetic analysis indicated that vB_HM387 has homologs, but vB_HM795 is a novel Myovirus, suggesting the heterogeneity of Burkholderia phages in melioidosis patients. The key finding that Burkholderia phages could be isolated from the blood of melioidosis patients highlights the potential application of phage-based assays by detecting phages in blood as a pathogen-derived biomarker of infection.

Metal Cross-Linked Supramolecular Gel Noodles: Structural Insights and Antibacterial Assessment.

Achieving precise control over gelator alignment and morphology is crucial for crafting tailored materials and supramolecular structures with distinct properties. We successfully aligned the self-assembled micelles formed by a functionalized dipeptide 2NapFF into long 1-D "gel noodles" by cross-linking with divalent metal chlorides. We identify the most effective cross-linker for alignment, enhancing mechanical stability, and imparting functional properties. Our study shows that Group 2 metal ions are particularly suited for creating mechanically robust yet flexible gel noodles because of their ionic and nondirectional bonding with carboxylate groups. In contrast, the covalent nature and high directional bonds of d-block metal ions with carboxylates tend to disrupt the self-assembly of 2NapFF. Furthermore, the 2NapFF-Cu noodles demonstrated selective antibacterial activity, indicating that the potent antibacterial property of the copper(II) ion is preserved within the cross-linked system. By merging insights into molecular alignment, gel extrusion processing, and integrating specific functionalities, we illustrate how the versatility of dipeptide-based gels can be utilized in creating next-generation soft materials.

Nanoscale assembly of enantiomeric supramolecular gels driven by the nature of solvents.

Understanding the key parameters that control the self-assembly process is critical to predict self-assembly modes in multi-component systems, which will lead to the development of nanofibrous materials with tuneable properties. Enantiomeric amino acid-based low-molecular-weight gelators (LMWGs) were mixed in polar (polar protic) and aromatic apolar (aromatic) solvents and compared to their individual counterparts to probe the effect of solvent polarity on the self-assembly process. Scanning electron microscopy (SEM) reveals that xerogels of individual components display hollow needles in polar protic solvents, while chiral coils are observed in aromatic solvents. In contrast, the multi-component gel displays hollow needle morphologies in both solvents, indicating similar morphologies in polar protic solvents but an entirely different nanostructure for the individual gel networks in aromatic solvents. PXRD experiments performed on the dried gels showed that the nature of the solvents plays a vital role in the co-assembly process of multi-component gels. The self-assembly modes and the gel state structure of the gels are analysed by wide-angle X-ray diffraction (WAXS) and small-angle neutron diffraction (SANS), which reveals that the mixed gel undergoes different co-assembly modes depending on the nature of the solvent systems. This study shows that different co-assembly modes can be achieved for structurally similar components by varying the solvent polarity, demonstrating the importance of solvent choice in the self-assembly process of multi-component gels.

Soft Materials with Time-Programmed Changes in Physical Properties through Lyotropic Phase Transitions Induced by pH-Changing Reactions.

We present the development of time-programmable functional soft materials. The materials undergo reversible phase transitions between lyotropic phases with different topologies and symmetries, which in turn have very different physical properties: viscosity, diffusion, and optical transparency. Here, this behavior is achieved by combining pH-responsive lyotropic phases made from the lipid monoolein doped with 10% oleic acid, with chemical reactions that have well-defined controllable kinetics: autocatalytic urea-urease and methyl formate hydrolysis, which increase and decrease pH, respectively. In this case, we use small-angle X-ray scattering (SAXS) and optical imaging to show temporally controlled transitions between the cloudy hexagonal phase, which is a two-dimensional (2D) array of cylindrical inverse micelles, and the transparent, highly viscous three-dimensional (3D) bicontinuous cubic phases. By combining these into a single reaction mixture where the pH increases and then decreases again, we can induce a sequential transformation cycle from hexagonal to cubic and back to hexagonal over several hours. The sample therefore changes from cloudy to transparent and back again as a proof-of-concept demonstration for a wider range of soft materials with time-programmable changes in physical properties.

Atomic structures of naphthalene dipeptide micelles unravel mechanisms of assembly and gelation.

Peptide-based biopolymers have gained increasing attention due to their versatile applications. A naphthalene dipeptide (2NapFF) can form chirality-dependent tubular micelles, leading to supramolecular gels. The precise molecular arrangement within these micelles and the mechanism governing gelation have remained enigmatic. We determined, at near-atomic resolution, cryoelectron microscopy structures of the 2NapFF micelles LL-tube and LD-tube, generated by the stereoisomers (l,l)-2NapFF and (l,d)-2NapFF, respectively. The structures reveal that the fundamental packing of dipeptides is driven by the systematic π-π stacking of aromatic rings and that same-charge repulsion between the carbonyl groups is responsible for the stiffness of both tubes. The structural analysis elucidates how a single residue's altered chirality gives rise to markedly distinct tubular structures and sheds light on the mechanisms underlying the pH-dependent gelation of LL- and LD-tubes. The understanding of dipeptide packing and gelation mechanisms provides insights for the rational design of 2NapFF derivatives, enabling the modulation of micellar dimensions.

A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen.

Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989-2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.

Summertime oxidative potential of atmospheric PM2.5 over New Delhi: Effect of aerosol ageing.

Exposure to elevated particulate matter (PM) concentrations in ambient air has become a major health concern over urban areas worldwide. Reactive oxygen species (ROS) generation due to ambient PM (termed as their oxidative potential, OP) is shown to play a major role in PM-induced health effects. In the present study, the OP of the ambient PM2.5 samples, collected during summer 2019 from New Delhi, were measured using the dithiothreitol (DTT) assay. Average volume-normalized OP (OPV) was 2.9 ± 1.1 nmol DTT min-1 m-3, and mass-normalized OP (OPm) was 61 ± 29 pmol DTT min-1 µg-1. The regression statistics of OPv vs chemical species show the maximum slope of OPV with the elemental carbon (EC, r2 = 0.72) followed by water-soluble organic carbon (WSOC, r2 = 0.72), and organic carbon (OC, r2 = 0.64). A strong positive correlation between OPm and secondary inorganic aerosols (SIA, such as NH4+ and NO3- mass fractions) was also observed, indicating that the sources emitting NO2 and NH3, precursors of NO3- and NH4+, also emit DTT-active species. Interestingly, the slope value of OPv vs OC for aged aerosols (OM/OC > 1.7, f44 > 0.12 and f43 < 0.04) was 1.7 times higher than relatively fresh organic aerosols (OA, OM/OC < 1.7, f44 < 0.12, f43 > 0.04). An increase in OPv and OPoc with f44 indicates the formation of more DTT active species with the ageing of OA. A linear increase in OPoc with increasing Nitrogen/Carbon (N/C) ratio suggests that nitrogenous OA have higher OP.

Human risk to tick encounters in the southeastern United States estimated with spatial distribution modeling.

Expanding geographic distribution and increased populations of ticks has resulted in an upsurge of human-tick encounters in the United States (US), leading to an increase in tickborne disease reporting. Limited knowledge of the broadscale spatial range of tick species is heightened by a rapidly changing environment. Therefore, we partnered with the Forest Inventory and Analysis (FIA) program of the Forest Service, U.S. Department of Agriculture and used passive tick surveillance to better understand spatiotemporal variables associated with foresters encountering three tick species (Amblyomma americanum L., Dermacentor variabilis Say, and Ixodes scapularis L.) in the southeastern US. Eight years (2014-2021) of tick encounter data were used to fit environmental niche and generalized linear models to predict where and when ticks are likely to be encountered. Our results indicate temporal and environmental partitioning of the three species. Ixodes scapularis were more likely to be encountered in the autumn and winter seasons and associated with soil organic matter, vegetation indices, evapotranspiration, temperature, and gross primary productivity. By contrast, A. americanum and D. variabilis were more likely to be encountered in spring and summer seasons and associated with elevation, landcover, temperature, dead belowground biomass, vapor pressure, and precipitation. Regions in the southeast least suitable for encountering ticks included the Blue Ridge, Mississippi Alluvial Plain, and the Southern Florida Coastal Plain, whereas suitable regions included the Interior Plateau, Central Appalachians, Ozark Highlands, Boston Mountains, and the Ouachita Mountains. Spatial and temporal patterns of different tick species can inform outdoorsmen and the public on tick avoidance measures, reduce tick populations by managing suitable tick habitats, and monitoring areas with unsuitable tick habitat for potential missed encounters.

Reversibly Tuning the Viscosity of Peptide-Based Solutions Using Visible Light.

Light can be used to design stimuli-responsive systems. We induce transient changes in the assembly of a low molecular weight gelator solution using a merocyanine photoacid. Through our approach, reversible viscosity changes can be achieved via irradiation, delivering systems where flow can be controlled non-invasively on demand.

Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles.

Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation and interspecies and interkingdom communication. However, the factors that regulate their release and heterogeneity are not well understood. We set out to investigate these factors in the common gut commensal Bacteroides thetaiotaomicron by studying BEV release throughout their growth cycle. Utilising a range of methods, we demonstrate that vesicles released at different stages of growth have significantly different composition, with early vesicles enriched in specifically released outer membrane vesicles (OMVs) containing a larger proportion of lipoproteins, while late phase BEVs primarily contain lytic vesicles with enrichment of cytoplasmic proteins. Furthermore, we demonstrate that lipoproteins containing a negatively charged signal peptide are preferentially incorporated in OMVs. We use this observation to predict all Bacteroides thetaiotaomicron OMV enriched lipoproteins and analyse their function. Overall, our findings highlight the need to understand media composition and BEV release dynamics prior to functional characterisation and define the theoretical functional capacity of Bacteroides thetaiotaomicron OMVs.

Correction: Multi-layer 3D printed dipeptide-based low molecular weight gels.

Correction for 'Multi-layer 3D printed dipeptide-based low molecular weight gels' by Max J. S. Hill et al., Soft Matter, 2022, 18, 5960-5965, https://doi.org/10.1039/D2SM00663D.

Fitting mathematical functions to extended lactation curves and forecasting late-lactation milk yields of dairy cows.

A 305-d lactation followed by a 60-d dry period has traditionally been considered economically optimal, yet dairy cows in modern intensive dairy systems are frequently dried off while still producing significant quantities of milk. Managing cows for an extended lactation has reported production, welfare, and economic benefits, but not all cows are suitable for an extended lactation. Implementation of an extended lactation strategy on-farm could benefit from use of a decision support system, based on a mathematical lactation model, that can identify suitable cows during early lactation that have a high likelihood of producing above a target milk yield (MY) at 305 d in milk (DIM). Therefore, our objectives were (1) to compare the suitability of 3 commonly used lactation models for modeling extended lactations (Dijkstra, Wood, and Wilmink) in primiparous and multiparous cows under a variety of lactation lengths, and (2) to determine the amount of early-lactation daily MY data needed to accurately forecast MY at d 305 by using the most suitable model and determine whether this is sufficient for identifying cows suitable for an extended lactation before the end of a typical voluntary waiting period (50-90 d). Daily MY data from 467 individual Holstein-Friesian lactations (DIM >305 d; 379 ± 65-d lactation length [mean ± SD]) were fitted by the 3 lactation models using a nonlinear regression procedure. The parameter estimates of these models, lactation characteristics (peak yield, time to peak yield, and persistency), and goodness-of-fit were compared between parity and different lactation lengths. The models had similar performance, and differences between parity groups were consistent with previous literature. Then, data from only the first i DIM for each individual lactation, where i was incremented by 30 d from 30 to 150 DIM and by 50 d from 150 to 300 DIM, were fitted by each model to forecast MY at d 305. The Dijkstra model was selected for further analysis, as it had superior goodness-of-fit statistics for i= 30 and 60. The data set was fit twice by the Dijkstra model, with parameter bounds either unconstrained or constrained. The quality of predictions of MY at d 305 improved with increasing data availability for both models and assisting the model fitting procedure with more biologically relevant constraints on parameters improved the predictions, but neither was reliable enough for practical use on-farm due to the high uncertainty of forecasted predictions. Using 90 d of data, the constrained model correctly classified 66% of lactations as being above or below a target MY at d 305 of 25 kg/d, with a probability threshold of 0.95. The proportion of correct classifications became smaller at lower targets of MY at d 305 and became greater when using more lactation days. Overall, further work is required to develop a model that can forecast late-lactation MY with sufficient accuracy for practical use. We envisage that a hybridized machine learning and mechanistic model that incorporates additional historical and genetic information with early-lactation MY could produce meaningful lactation curve forecasts.

Genomic characterization of colistin-resistant Klebsiella pneumoniae isolated from intensive care unit patients in Egypt.

BACKGROUND: Egypt has witnessed elevated incidence rates of multidrug-resistant Klebsiella pneumoniae infections in intensive care units (ICUs). The treatment of these infections is becoming more challenging whilst colistin-carbapenem-resistant K. pneumoniae is upsurging. Due to the insufficiently available data on the genomic features of colistin-resistant K. pneumoniae in Egypt, it was important to fill in the gap and explore the genomic characteristics, as well as the antimicrobial resistance, the virulence determinants, and the molecular mechanisms of colistin resistance in such a lethal pathogen. METHODS: Seventeen colistin-resistant clinical K. pneumoniae isolates were collected from ICUs in Alexandria, Egypt in a 6-month period in 2020. Colistin resistance was phenotypically detected by modified rapid polymyxin Nordmann/Poirel and broth microdilution techniques. The isolates susceptibility to 20 antimicrobials was determined using Kirby-Bauer disk diffusion method. Whole genome sequencing and bioinformatic analysis were employed for exploring the virulome, resistome, and the genetic basis of colistin resistance mechanisms. RESULTS: Out of the tested K. pneumoniae isolates, 82.35% were extensively drug-resistant and 17.65% were multidrug-resistant. Promising susceptibility levels towards tigecycline (88.24%) and doxycycline (52.94%) were detected. Population structure analysis revealed seven sequence types (ST) and K-types: ST383-K30, ST147-K64, ST17-K25, ST111-K63, ST11-K15, ST14-K2, and ST525-K45. Virulome analysis revealed yersiniabactin, aerobactin, and salmochelin siderophore systems in ˃ 50% of the population. Hypervirulence biomarkers, iucA (52.94%) and rmpA/A2 (5.88%) were detected. Extended-spectrum ß-lactamase- and carbapenemase-producers accounted for 94.12% of the population, with blaCTX-M-15, blaNDM-5, and blaOXA-48 reaching 64.71%, 82.35%, and 82.35%, respectively. Chromosomal alterations in mgrB (82.35%) were the most prevailing colistin resistance-associated genetic change followed by deleterious mutations in ArnT (23.53%, L54H and G164S), PmrA (11.76%, G53V and D86E), PmrB (11.76%, T89P and T134P), PmrC (11.76%, S257L), PhoQ (5.88%, L322Q and Q435H), and ArnB (5.88%, G47D) along with the acquisition of mcr-1.1 by a single isolate of ST525. CONCLUSIONS: In this study, we present the genotypic colistin resistance mechanisms in K. pneumoniae isolated in Egypt. More effective antibiotic stewardship protocols must be implemented by Egyptian health authorities to restrain this hazard and safeguard the future utility of colistin. This is the first characterization of a complete sequence of mcr-1.1-bearing IncHI2/IncHI2A plasmid recovered from K. pneumoniae clinical isolate belonging to the emerging high-risk clone ST525.

Effect of Imposing Spatial Constraints on Low Molecular Weight Gels.

We outline the effect of imposing spatial constraints during gelation on hydrogels formed by dipeptide-based low molecular weight gelators. The gels were formed via either a solvent switch or a change in pH and formed in different sized vessels to produce gels of different thickness while maintaining the same volume. The different methods of gelation led to gels with different underlying microstructure. Confocal microscopy was used to visualize the resulting microstructures, while the corresponding mechanical properties were probed via cavitation rheology. We show that solvent-switch-triggered gels are sensitive to imposed spatial constraints, in both altered microstructure and mechanical properties, while their pH-triggered equivalents are not. These results are significant because it is often necessary to form gels of different thicknesses for different analytical techniques. Also, gels of different thicknesses are utilized between various applications of these materials. Our data show that it is important to consider the spatial constraints imposed in these situations.

Multi-locus homozygosity promotes actuarial senescence in a wild mammal.

Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.

Investigating multigelator systems across multiple length scales.

Preparation of multicomponent systems provides a method for changing the properties of low molecular weight gelator (LMWG)-based systems. Here we have prepared a variety of multicomponent systems where both components are N-functionalised dipeptide-based LMWGs that may either co-assemble or self-sort when mixed. We exemplify how varying the concentration ratio of the two components can be used to tune the properties of the multicomponent systems pre-gelation, during gelation and in the gel state using viscosity and rheology measurements, circular dichroism, NMR and small angle neutron scattering. We also investigate the effect of changing the chirality of a single component on the properties of these systems. While predicting the outcome of multicomponent assembly is a challenge, the preparation of a variety of systems allows us to probe the factors affecting their design. This work provides insights into how the properties of multicomponent systems composed of two gelators with the same basic structural design can be tuned by varying the chirality and the concentration ratio of the two components and considering the behaviour of the two components when alone.

Self-Sorting in Diastereomeric Mixtures of Functionalized Dipeptides.

Self-sorting in functionalized dipeptide systems can be driven by the chirality of a single amino acid, both at a high pH in the micellar state and at a low pH in the gel state. The structures formed are affected to some degree by the relative concentrations of each component showing the complexity of such an approach. The structures underpinning the gel network are predefined by the micellar structures at a high pH. Here, we describe the systems prepared from two dipeptide-based gelators that differ only by the chirality of one of the amino acids. We provide firm evidence for self-sorting in the micellar and gel phases using small-angle neutron scattering and cryo-transmission electron microscopy (cryo-TEM), showing that complete self-sorting occurs across a range of relative concentrations.

Photothermal Perylene Bisimide Hydrogels.

Gels formed using a perylene bisimide (PBI) as a low molecular weight gelator can show the photothermal effect. Formation of the PBI radical anion results in new absorption bands forming, meaning that subsequent irradiation with a wavelength of light overlapping with the new absorption band leads to heating of the gel. This approach can be used to heat the gel, as well as the surrounding milieu. We show how we can use electrochemical methods as well as multicomponent systems to form the radical anion without the need for UV light, and how we can use the photothermal effect to induce phase transitions in the solutions above the gels by exploiting photothermal behavior.