Cluster Population Research Articles

Genome-wide association study of the loci and candidate genes associated with agronomic traits in Amomum villosum Lour.

Amomum villosum Lour. (A. villosum) is a valuable herbaceous plant that produces the famous traditional Chinese medicine Amori Fructus. Identifying molecular markers associated with the growth of A. villosum can facilitate molecular marker-assisted breeding of the plant. This study employed 75 A. villosum accessions as the test material and utilized 71 pairs of polymorphic simple sequence repeat (SSR) molecular markers to genotype the population. The study analyzed the association between SSR markers and phenotypic traits through the linkage imbalance and population structure analysis. Candidate genes associated with the molecular markers were also identified. The results showed that the phenotypic diversity index range of the 12 agronomic traits was 4.081-4.312 and conformed to a normal distribution. Moreover, 293 allelic variations were detected in the 75 accessions, with an average of 5.32 amplified alleles per loci, ranging from 3 to 8. The maximum number of amplified alleles for AVL12 was 8. The population structure and cluster analysis indicated that the accessions could be divided into two subgroups. Using the mixed linear model (MLM) model of population structure (Q)+kinship matrix (K) for association analysis, three SSR molecular markers significantly associated with the agronomic traits were detected. Fluorescence quantification was used to analyze the expression levels of six candidate genes, and it was found that three of the genes were differentially expressed in phenotypically different accessions. This study is the first to use SSR markers for genome-wide association study (GWAS) mapping and identification of the associated agronomic traits in A. villosum. The results of this study provide a basis for identifying genetic markers for growth traits for marker-assisted breeding in A. villosum.

Abstract We018: The Molecular Mechanism of Coronary Collateral Growth Induced by Repetitive Ischemia by Single Cell-RNA Sequencing

Coronary heart diseases (CHD) are the leading cause of mortality and morbidity in the United States. A well-developed coronary collateral circulation ameliorates the consequences of CHD, reducing the incidence of sudden death and infarct sizes following coronary occlusion. Stimulation of coronary collateral growth (CCG) is also an alternative therapeutic approach for patients with intractable angina pectoris. The importance of CCG is undisputable, but the process and mechanism underlying the CCG is unclear. We developed a mouse model of CCG by repetitive ischemia (RI) in adults, and the CCG was validated with contrast echo to measure the coronary blood flow 3D images of micro-CT to quantitate the CCG. In this study, we use single cell-RNA sequencing (scRNA-Seq) to analyze the molecular signaling of CCG at different time points during the RI process. We digested the hearts from RI days 5, 10, and 17 and control (naïve) mice, harvested non-cardiomyocytes, performed scRNA-Seq with 10x Genomics and sequenced with Next-Seq 500 (Illumina).The fastq files are converted to a gene count matrix using kallisto|bustools with refdata-gex-mm10-2020-A employed as the reference mouse genome. The Kallisto bustools output is then converted in R to files compatible for uploading to Cellenics, an open-source platform for single-cell RNA-Seq analysis. Dimensionality reduction is done with Principal Components Analysis (PCA) with 30 principal components. We will use UMAP to visualize cell clusters. Cellenics uses scType to annotate the cell populations automatically when building clusters of cell populations. Our preliminary data show dynamic kinetics of non-cardiomyocytes induced by RI over the timeline of CCG and different cell populations of non-cardiomyocytes and EC expression profiling varied in response to RI throughout CCG. We will validate the critical signaling in CCG and explore the potential targets to induce CCG.

Assessing radon hazard in drinking water: A comprehensive approach integrating deterministic and probabilistic methods with water consumption routines

The research aimed to determine the spatiotemporal distribution patterns of radon activity concentrations in tap water of Yerevan city and assess radon-associated hazards using both deterministic and probabilistic approaches. This was accomplished by integrating one-year monitoring data of radon in water with water consumption habits among adult population clusters, which were identified through food frequency questionnaire in Yerevan.The study findings indicated variations in radon activity levels across administrative districts. The highest average activity concentrations were detected in Davtashen (7.07 Bq/L), while the lowest average was observed in Kanaker-Zeytun (1.57 Bq/L). The overall pattern of spatiotemporal variation during monitoring period revealed higher prevalence of radon in water in the northern and western parts of the city compared to the east and south, indicating different sources of drinking water. The radon-associated hazard assessment from water, using a deterministic approach (e.g., inhalation, ingestion, radon dissolution in blood, total effective dose), revealed values below the individual dose criterion (IDC) of 0.1 mSv/y. Monte Carlo simulation revealed a probability of exceeding IDC in specific water consumption-based groups. Residents of Yerevan who drink more than 3 L water daily with the highest observed activity concentration of 11.4 Bq/L, have an 86.26 % chance of exceeding IDC. Residents consuming 2.1 L water daily have a 7.02 % chance of exceeding IDC.The study highlights the importance of applied principles and methodologies for radon monitoring, particularly considering actual water consumption data and different risk assessment approaches. Considering the worst-case scenario results, it is recommended to keep tap water consumption up to 3 L per day, keeping the tap open longer to reduce radon levels. It also emphasizes the need for continued monitoring, given the variations in radon activity. The study provides valuable insights into radon exposure assessment, mitigation, and action plans in terms of water safety and public health.

Assessing Cross-Contamination in Spike-Sorted Electrophysiology Data.

Recent advances in extracellular electrophysiology now facilitate the recording of spikes from hundreds or thousands of neurons simultaneously. This has necessitated both the development of new computational methods for spike sorting and better methods to determine spike-sorting accuracy. One long-standing method of assessing the false discovery rate (FDR) of spike sorting-the rate at which spikes are assigned to the wrong cluster-has been the rate of interspike interval (ISI) violations. Despite their near ubiquitous usage in spike sorting, our understanding of how exactly ISI violations relate to FDR, as well as best practices for using ISI violations as a quality metric, remains limited. Here, we describe an analytical solution that can be used to predict FDR from the ISI violation rate (ISIv). We test this model in silico through Monte Carlo simulation and apply it to publicly available spike-sorted electrophysiology datasets. We find that the relationship between ISIv and FDR is highly nonlinear, with additional dependencies on firing frequency, the correlation in activity between neurons, and contaminant neuron count. Predicted median FDRs in public datasets recorded in mice were found to range from 3.1 to 50.0%. We found that stochasticity in the occurrence of ISI violations as well as uncertainty in cluster-specific parameters make it difficult to predict FDR for single clusters with high confidence but that FDR can be estimated accurately across a population of clusters. Our findings will help the growing community of researchers using extracellular electrophysiology assess spike-sorting accuracy in a principled manner.

JWST Photometry of Globular Clusters in A2744. II. Luminosity and Color Distributions

Deep JWST imaging of the giant galaxy cluster A2744, at redshift z = 0.308, is used to explore the features of its rich population of globular clusters (GCs), building on our initial survey of the system. We use the photometry of more than 10,000 GCs over a 3 mag range to construct the GC luminosity function and color distribution. These results now specifically account for photometric incompleteness as a function of location relative to the five giant galaxies that dominate the gravitational potential of A2744. The total GC population in A2744 is estimated at N GC ≥ 1.1 × 105, consistent with its high total mass. We also directly compare the observed distributions with theoretical predictions for GC populations drawn from the recent EMP-Pathfinder simulations, viewed at the same 3.5 Gyr look-back time as the cluster. The simulations match the observations well, with the only notable disagreement being that the simulations predict larger numbers of GCs at high metallicity formed after z ≃ 2 than are seen in the data.

Association Mapping of Seed Coat Color Characteristics for Near-Isogenic Lines of Colored Waxy Maize Using Simple Sequence Repeat Markers.

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize.

Species distribution models predict genetic isolation of Hetaerina vulnerata Hagen in Selys, 1853 (Odonata, Calopterygidae).

Understanding how past and current environmental conditions shape the demographic and genetic distributions of organisms facilitates our predictions of how future environmental patterns may affect populations. The Canyon Rubyspot damselfly (Odonata: Zygoptera: Hetaerina vulnerata) is an insect with a range distribution from Colombia to the arid southwestern United States, where it inhabits shaded mountain streams in the arid southwestern United States. Past spatial fragmentation of habitat and limited dispersal capacity of H. vulnerata may cause population isolation and genetic differentiation, and projected climate change may exacerbate isolation by further restricting the species' distribution. We constructed species distribution models (SDMs) based on occurrences of H. vulnerata and environmental variables characterizing the species' niche. We inferred seven current potential population clusters isolated by unsuitable habitat. Paleoclimate models indicated habitat contiguity in past conditions; projected models indicated some habitat fragmentation in future scenarios. Seventy-eight H. vulnerata individuals from six of the current clusters were sequenced via ddRADseq and processed with Stacks. Principal components and phylogeographic analyses resolved three subpopulations; Structure resolved four subpopulations. F ST values were low (<0.05) for nearby populations and >0.15 for populations separated by expanses of unsuitable habitat. Isolation by distance was an existing but weak factor in determining genomic structure; isolation by environment and the intervening landscape explained a significant proportion of genetic distance. Hetaerina vulnerata populations were shown to be isolated by a lack of tree canopy coverage, an important habitat predictor for oviposition and territoriality. Thus, H. vulnerata populations are likely separated and are genetically isolated. Integrating SDMs with landscape genetics allowed us to identify populations separated by distance and unsuitable habitat, explaining population genetic patterns and probable fates for populations under future climate scenarios.

The PARSEC view of star formation in galaxy centres: from protoclusters to star clusters in an early-type spiral

ABSTRACT Understanding star formation in galaxies requires resolving the physical scale on which star formation often occurs: the scale of star clusters. We present a multiwavelength, eight-parsec resolution study of star formation in the circumnuclear star cluster and molecular gas rings of the early-type spiral NGC 1386. The cluster ring formed simultaneously ∼4 Myr ago. The clusters have similar properties in terms of mass and star formation rate, resembling those of H ii regions in the Milky Way disc. The molecular CO gas resolves into long filaments, which define a secondary ring detached from the cluster ring. Most clusters are in CO voids. Their separation with respect to the CO filaments is reminiscent of that seen in galaxy spiral arms. By analogy, we propose that a density wave through the disc of this galaxy may have produced this gap in the central kpc. The CO filaments fragment into strings of dense, unresolved clouds with no evidence of a stellar counterpart. These clouds may be the sites of a future population of clusters in the ring. The free-fall time of these clouds, ∼10 Myr, is close to the orbital time of the CO ring. This coincidence could lead to a synchronous bursting ring, as is the case for the current ring. The inward spiralling morphology of the CO filaments and co-spatiality with equivalent kpc-scale dust filaments are suggestive of their role as matter carriers from the galaxy outskirts to feed the molecular ring and a moderately active nucleus.

Cluster population demographics in NGC 628 derived from stochastic population synthesis models

ABSTRACT The physical properties of star cluster populations offer valuable insights into their birth, evolution, and disruption. However, individual stars in clusters beyond the nearest neighbours of the Milky Way are unresolved, forcing analyses of star cluster demographics to rely on integrated light, a process fraught with uncertainty. Here, we infer the demographics of the cluster population in the benchmark galaxy NGC 628 using data from the Legacy Extra-galactic UV Survey (LEGUS) coupled to a novel Bayesian forward-modelling technique. Our method analyses all 1178 clusters in the LEGUS catalogue, $\sim 4$ times more than prior studies severely affected by completeness cuts. Our results indicate that the cluster mass function is either significantly steeper than the commonly observed slope of $-2$ or is truncated at $\approx 10^{4.5}$ M$_\odot$; the latter possibility is consistent with proposed relations between truncation mass and star formation surface density. We find that cluster disruption is relatively mild for the first $\approx 200$ Myr of cluster evolution; no evidence for mass-dependent disruption is found. We find suggestive but not incontrovertible evidence that inner galaxy clusters may be more prone to disruption and outer galaxy clusters have a more truncated mass function, but confirming or refuting these findings will require larger samples from future observations of outer galaxy clusters. Finally, we find that current stellar track and atmosphere models, along with common forms for cluster mass and age distributions, cannot fully capture all features in the multidimensional photometric distribution of star clusters. While our forward-modelling approach outperforms earlier backward-modelling approaches, some systematic differences persist between observed and modelled photometric distributions.

On the Origin of Fast-rotating Stars. I. Photometric Calibration and Results of AO-assisted BVRI+Hα Imaging of NGC 330 with SAMI/SOAR

Hα emission is a clear indicator of circumstellar activity in Be stars, historically employed to assess the classical Be star (CBe) population in young open clusters (YOCs). The YOC NGC 330 in the Small Magellanic Cloud exhibits a large known fraction of CBe stars and was selected for a pilot study to establish a comprehensive methodology for identifying Hα emitters in the Magellanic Clouds, encompassing the entire B-type spectral range. Using the SOAR Adaptive Module Imager (SAMI), we investigated the stellar population of NGC 330 using multiband BVRI+Hα imaging. We identified Hα emitters within the entire V-band range covered by SAMI/SOAR observations (V ≲ 22), comprising the complete B-type stellar population and offering a unique opportunity to explore the Be phenomenon across all spectral subclasses. The stellar radial distribution shows a clear bimodal pattern between the most massive (B5 or earlier) and the lower mass main-sequence objects (later than B6) within the cluster. The former is concentrated toward the cluster center (showing a dispersion of σ = 4.26 ± 0.20 pc), whereas the latter extends across larger radii (σ = 10.83 ± 0.65 pc), indicating mass stratification within NGC 330. The total fraction of emitters is 4.4% ± 0.5%, notably smaller than previous estimates from flux- or seeing-limited observations. However, a higher fraction of Hα emitters is observed among higher mass stars (32.8% ± 3.4%) than within lower mass (4.4% ± 0.9%). Consequently, the putative CBe population exhibits distinct dynamical characteristics compared to the bulk of the stellar population in NGC 330. These findings highlight the significance of the current observations in providing a complete picture of the CBe population in NGC 330.

The Great Rift Valley is a more pronounced biogeographic barrier than the Blue Nile Valley for six Ethiopian Highland passerines in the eastern Afromontane biodiversity hotspot

ABSTRACT The Ethiopian Highlands are divided by lowland biogeographic barriers, including the Blue Nile Valley (BNV) and Great Rift Valley (GRV). We show that the GRV is a more pronounced phylogeographic break than the BNV for 6 focal passerines. Previous research suggests that the BNV greatly shaped phylogeographic patterns in relatively sedentary montane taxa such as frogs and rodents, whereas the GRV shaped phylogeographic patterns in volant taxa such as birds. However, no previous research simultaneously compares the impact of each valley on phylogeographic patterns in birds, and as these barriers vary in geographic extent and topography, the relative extent of their effects on gene flow is unclear. Using whole-genome resequencing, we quantified genetic variation in 6 montane forest passerines in the Ethiopian Highlands and found that their phylogeographic patterns varied, with general trends distinct from those of taxa that were previously studied across the same barriers. Genetic variation was assessed by estimating genome-wide genetic diversity (HO), demographic history, phylogeographic structure, and phylogeographic concordance among taxa. Population pairs flanking the GRV showed higher FST and more distinct population clusters in principal component analysis than those separated by the BNV. HO was broadly consistent across populations, excluding noticeable reductions in 2 populations (1 population each in 2 separate species). The overall phylogenetic signature and concordance across study taxa supported populations separated by the BNV as sister and populations southeast of the GRV as most distinct.

Landscape and conservation genetics of western black crested gibbons (Nomascus concolor) in China.

Despite decades of field study, very little is known about the molecular ecology of gibbons, particularly as it relates to their ability to disperse across degraded and fragmentary landscapes. The critically endangered western black crested gibbon (Nomascus concolor) has been reduced to a small, fragmented population with about 1300 individuals. In the largest population genetic study of free-ranging gibbons to date, we sampled 47 of these gibbons from 13 sites in China and generated 15 polymorphic autosomal microsatellite markers. We identify three population clusters of N. concolor in Yunnan centered in 1) the Wuliang and Ailao Mountains, 2) the Yongde Daxueshan Mountains, and 3) an isolated remnant near the border with Vietnam. Within the Wuliang Mountains, we identified four subclusters, three of which are bounded by high-altitude rhododendron forest, and one that is isolated from the main population by ~2 km of degraded forest and pasture. Least-cost path analysis and isolation by resistance modeling demonstrates that the population genetic distances among gibbons in Wuliangshan National Nature Reserve are significantly correlated with geographic paths that avoid use of high-altitude rhododendron forest in favor of evergreen broadleaf forest. Although these gibbons have likely undergone reductions in heterozygosity from recent consanguineous mating, we suggest that their active avoidance of inbreeding on the population level maintains higher than expected levels of genetic diversity. This research provides new insights into how gibbons interact with heterogeneous environments and expands our understanding of their molecular ecology and conservation genetics.

Safety and effectiveness of a recombinant hepatitis E vaccine in women of childbearing age in rural Bangladesh: a phase 4, double-blind, cluster-randomised, controlled trial

Hepatitis E virus (HEV) leads to high mortality in pregnant women in low-income countries. We aimed to evaluate the safety of a HEV vaccine and its effectiveness in preventing hepatitis E during pregnancy. In this phase 4, double-blind, cluster-randomised trial, 67 villages in Matlab, Bangladesh, were randomised 1:1 to receive HEV239 (a recombinant HEV vaccine) or a control vaccine (Hepa-B, a hepatitis B vaccine), using block randomisation with random number tables and blocks of size eight, stratified by cluster population size. Eligible non-pregnant women (aged 16-39 years) were vaccinated intramuscularly on day 0, at 1 month, and at 6 months, and followed up for 2 years after the last immunisation. The primary endpoint was hepatitis E in the pregnant, per-protocol population (those who received all three doses within 2 days of the scheduled dates), while safety was a secondary endpoint, assessed in the intention-to-treat (ITT) population (participants who received at least one dose). Solicited adverse events were recorded for the first 7 days after each dose, and unsolicited events until 2 years after a participant's final dose. Pregnancy-related safety outcomes were assessed in the pregnant ITT population. This study is registered with ClinicalTrials.gov (NCT02759991). Between Oct 2, 2017, and Feb 28, 2019, 19 460 participants were enrolled and received either HEV239 (9478 [48·7%] participants, 33 clusters) or Hepa-B (9982 [51·3%] participants, 34 clusters), of whom 17 937 (92·2%) participants received three doses and 17 613 (90·5%) were vaccinated according to protocol (8524 [48·4%] in the HEV239 group and 9089 [51·6%] in the control group). No pregnant participants were confirmed to have hepatitis E in either treatment group. HEV239 showed a mild safety profile, similar to Hepa-B, with no difference in the proportion of solicited adverse events between groups and no severe solicited events. Pain was the most common local symptom (1215 [12·8%] HEV239 recipients and 1218 [12·2%] Hepa-B recipients) and fever the most common systemic symptom (141 [1·5%] HEV239 recipients and 145 [1·5%] Hepa-B recipients). None of the serious adverse events or deaths were vaccine related. Among pregnant participants, the HEV239 group had a higher risk of miscarriage (136 [5·7%] of 2407 pregnant participants) compared with the control group (102 [3·9%] of 2604; adjusted odds ratio 1·54 [95% CI 1·15-2·08]). The effectiveness of HEV239 in pregnant women remains uncertain. HEV239 was safe and well tolerated in non-pregnant women, but findings regarding miscarriage warrant further investigation. Research Council of Norway; Innovax.

Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay.

Plasmodium vivax is the most predominant malaria species in Latin America, constituting 71.5% of malaria cases in 2021. With several countries aiming for malaria elimination, it is crucial to prioritize effectiveness of national control programs by optimizing the utilization of available resources and strategically implementing necessary changes. To support this, there is a need for innovative approaches such as genomic surveillance tools that can investigate changes in transmission intensity, imported cases and sources of reintroduction, and can detect molecular markers associated with drug resistance. Here, we apply a modified highly-multiplexed deep sequencing assay: Pv AmpliSeq v2 Peru. The tool targets a newly developed 41-SNP Peru barcode for parasite population analysis within Peru, the 33-SNP vivaxGEN-geo panel for country-level classification, and 11 putative drug resistance genes. It was applied to 230 samples from the Peruvian Amazon (2007-2020), generating baseline surveillance data. We observed a heterogenous P. vivax population with high diversity and gene flow in peri-urban areas of Maynas province (Loreto region) with a temporal drift using all SNPs detected by the assay (nSNP = 2909). In comparison, in an indigenous isolated area, the parasite population was genetically differentiated (FST = 0.07-0.09) with moderate diversity and high relatedness between isolates in the community. In a remote border community, a clonal P. vivax cluster was identified, with distinct haplotypes in drug resistant genes and ama1, more similar to Brazilian isolates, likely representing an introduction of P. vivax from Brazil at that time. To test its applicability for Latin America, we evaluated the SNP Peru barcode in P. vivax genomes from the region and demonstrated the capacity to capture local population clustering at within-country level. Together this data shows that P. vivax transmission is heterogeneous in different settings within the Peruvian Amazon. Genetic analysis is a key component for regional malaria control, offering valuable insights that should be incorporated into routine surveillance.

Isolation and characterization of normal mandibular periosteal stem cells from human and macaca mulatta and cross-species single-cell analysis

Objective: To investigate the presence of a distinct stem cell populations different from mesenchymal stem cells in the mandibular periosteum of both human and non-human primates (macaca mulatta), to explore its properties during intramembranous osteogenesis and to establish standard protocols for the isolation, culturing and expanding of mandibular periosteal stem cells (PSC) distinguished from other PSCs in other anatomical regions. Methods: Periosteum was harvested from the bone surface during flap bone removal in patients aged 18-24 years undergoing third molar extraction and from the buccal side of the mandibular premolar region of 6-year-old macaca mulatta respectively, and then subjected to single-cell sequencing using the Illumina platform Novaseq 6000 sequencer. Cross-species single-cell transcriptome sequencing results were compared using homologous gene matching. PSC were isolated from primary tissues using two digestion methods with body temperature and low temperature, and their surface markers (CD200, CD31, CD45 and CD90) were identified by cell flow cytometry. The ability of cell proliferation and three-lineage differentiation of PSC expanded to the third generation in vitro in different species were evaluated. Finally, the similarities and differences in osteogenic properties of PSC and bone marrow mesenchymal stem cells (BMSC) were compared. Results: The single-cell sequencing results indicated that 18 clusters of cell populations were identified after homologous gene matching for dimensionality reduction, and manual cellular annotation was conducted for each cluster based on cell marker databases. The comparison of different digestion protocols proved that the low-temperature overnight digestion protocol can stably isolate PSC from the human and m. mulatta mandibular periosteum and the cells exhibited a fibroblast-like morphology. This research confirmed that PSC of human and m. mulatta had similar proliferation capabilities through the cell counting kit-8 assay. Flow cytometry analysis was then used to identify the cells isolated from the periosteum expressed CD200(+), CD31(-), CD45(-), CD90(-). Then, human and m. mulatta PSC were induced into osteogenesis, adipogenesis, and chondrogenesis to demonstrate their corresponding multi-lineage differentiation capabilities. Finally, comparison with BMSC further clarified the oesteogenesis characteristics of PSC. The above experiments proved that the cells isolated from the periosteum were peiosteal cells with characteristics of stem cells evidenced by their cell morphology, proliferation ability, surface markers, and differentiation ability, and that this group of PSC possessed characteristics different from traditional mesenchymal stem cells. Conclusions: In this study, normal mandibular PSC from humans and m. mulatta were stably isolated and identified for the first time, providing a cellular foundation for investigating the mechanism of mandibular intramembranous osteogenesis, exploring ideal non-human primate models and establishing innovative strategies for clinically mandibular injury repair.

K-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations.

One of the key challenges of k-means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as k-means++ have mitigated this limitation by estimating the centroids using an empirical probability distribution. However, with high-dimensional and complex data sets such as those obtained from molecular simulation, k-means++ fails to partition the data in an optimal manner. Furthermore, stochastic elements in all flavors of k-means++ will lead to a lack of reproducibility. K-means N-Ary Natural Initiation (NANI) is presented as an alternative to tackle this challenge by using efficient n-ary comparisons to both identify high-density regions in the data and select a diverse set of initial conformations. Centroids generated from NANI are not only representative of the data and different from one another, helping k-means to partition the data accurately, but also deterministic, providing consistent cluster populations across replicates. From peptide and protein folding molecular simulations, NANI was able to create compact and well-separated clusters as well as accurately find the metastable states that agree with the literature. NANI can cluster diverse data sets and be used as a standalone tool or as part of our MDANCE clustering package.

Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.

Molecular dynamics (MD) simulations are ideally suited to describe conformational ensembles of biomolecules such as proteins and nucleic acids. Microsecond-long simulations are now routine, facilitated by the emergence of graphical processing units. Clustering, which groups objects based on structural similarity, is typically used to process ensembles, leading to different states, their populations, and the identification of representative structures. A popular pipeline combines hierarchical clustering for clustering and selecting the cluster centroid as representative of the cluster. Here, we propose to improve on this approach, by developing a module-Protein Retrieval via Integrative Molecular Ensembles (PRIME), that consists of tools to improve the prediction of the representative in the most populated cluster using extended continuous similarity. PRIME is integrated with our Molecular Dynamics Analysis with N-ary Clustering Ensembles (MDANCE) package and can be used as a postprocessing tool for arbitrary clustering algorithms, compatible with several MD suites. PRIME predictions produced structures that when aligned to the experimental structure were better superposed (lower RMSD). A further benefit of PRIME is its linear scaling─rather than the traditional O(N2) traditionally associated with comparisons of elements in a set.

Genome resequencing reveals population divergence and local adaptation of blacklegged ticks in the United States.

Tick vectors and tick-borne disease are increasingly impacting human populations globally. An important challenge is to understand tick movement patterns, as this information can be used to improve management and predictive modelling of tick population dynamics. Evolutionary analysis of genetic divergence, gene flow and local adaptation provides insight on movement patterns at large spatiotemporal scales. We develop low coverage, whole genome resequencing data for 92 blacklegged ticks, Ixodes scapularis, representing range-wide variation across the United States. Through analysis of population genomic data, we find that tick populations are structured geographically, with gradual isolation by distance separating three population clusters in the northern United States, southeastern United States and a unique cluster represented by a sample from Tennessee. Populations in the northern United States underwent population contractions during the last glacial period and diverged from southern populations at least 50 thousand years ago. Genome scans of selection provide strong evidence of local adaptation at genes responding to host defences, blood-feeding and environmental variation. In addition, we explore the potential of low coverage genome sequencing of whole-tick samples for documenting the diversity of microbial pathogens and recover important tick-borne pathogens such as Borrelia burgdorferi. The combination of isolation by distance and local adaptation in blacklegged ticks demonstrates that gene flow, including recent expansion, is limited to geographical scales of a few hundred kilometres.

Recent evolution of the star cluster population in the Andromeda’s disk

The most accurate parameters of star clusters are determined by analyzing colour-magnitude diagrams (CMDs) constructed from their member stars. The recent study applying this method to the analysis of the Panchromatic Hubble Andromeda Treasury (PHAT) survey star clusters includes objects up to ages of 300 Myr. In this study, we aim to extend a sample of star clusters with parameters determined based on CMDs of individual stars to older ages, up to ~700 Myr. We have developed an isochrone fitting procedure for CMDs of resolved and semi-resolved clusters to determine their parameters. The Bayesian approach is employed in determining star cluster ages and interstellar extinctions. We determined ages and extinctions for a sample of 854 star clusters from the M31 PHAT survey. We found that the star formation rate in the M31 galaxy was rather constant during the last ~130 Myr; however, a strong cluster formation episode occurred ~220 Myr ago, and can be attributed to the predicted passage of the M32 galaxy through the Andromeda’s disk.

The heart of galaxy clusters: Demographics and physical properties of cool-core and non-cool-core halos in the TNG-Cluster simulation

We analyzed the physical properties of the gaseous intracluster medium (ICM) at the center of massive galaxy clusters with TNG-Cluster, a new cosmological magnetohydrodynamical simulation. Our sample contains 352 simulated clusters spanning a halo mass range of 1014 &lt; M500c/M⊙ &lt; 2 × 1015 at z = 0. We focused on the proposed classification of clusters into cool-core (CC) and non-cool-core (NCC) populations, the z = 0 distribution of cluster central ICM properties, and the redshift evolution of the CC cluster population. We analyzed the resolved structure and radial profiles of entropy, temperature, electron number density, and pressure. To distinguish between CC and NCC clusters, we considered several criteria: central cooling time, central entropy, central density, X-ray concentration parameter, and density profile slope. According to TNG-Cluster and with no a priori cluster selection, the distributions of these properties are unimodal, whereby CCs and NCCs represent the two extremes. Across the entire TNG-Cluster sample at z = 0 and based on the central cooling time, the strong CC fraction is fSCC = 24%, compared to fWCC = 60% and fNCC = 16% for weak and NCCs, respectively. However, the fraction of CCs depends strongly on both halo mass and redshift, although the magnitude and even direction of the trends vary with definition. The abundant statistics of simulated high-mass clusters in TNG-Cluster enabled us to match observational samples and make a comparison with data. The CC fractions from z = 0 to z = 2 are in broad agreement with observations, as are the radial profiles of thermodynamical quantities, globally as well as when divided as CC versus NCC halos. TNG-Cluster can therefore be used as a laboratory to study the evolution and transformations of cluster cores due to mergers, AGN feedback, and other physical processes.