Canonical Cluster Research Articles

Morphometric analyses as a tool for the delimitation of a species complex of rupicolous Cattleya orchids from the Brazilian campos rupestres of Minas Gerais and Bahia

In the present study we perform a linear morphometric analysis to assess species delimitation in Cattleya caulescens, C. pabstii, and C. pfisteri, which constitute a species complex in Brazilian campos rupestres. For this purpose, we collected 18 linear measurement variables from flowers of 153 individuals in 11 populations from the three species in the Brazilian States of Minas Gerais and Bahia. We applied Principal Component Analysis (PCA), Canonical Variate Analysis (CVA) and cluster analysis to assess the morphological variation between populations. The analyses indicated a clear difference and cohese clusters of populations for each species, but one of the populations of C. pfisteri was divergent from the other populations. This difference is putatively explained by genetic data from other studies that suggest introgression from a species from a different series, C. sincorana, in this location. The differences between C. caulescens and C. pabstii reinforce the floristic differentiation of the orchid flora from the quartzitic mountains of Southern Minas Gerais in relation to the Espinhaço range to the north, as well as the development of a specialized orchid flora in the iron ore outcrops in Central Minas Gerais.

A global assemblage of tax haven clusters: profit shifting, tax dodging and money laundering

In this paper we explore a selection of tax haven clusters in the US and Europe as diverse but recognisable species of some fifty of the phenomena worldwide that have been seldom studied from an economic geography or spatial planning viewpoint. We treat the objects of study as being almost perfect expressions of the classical, canonical cluster configuration. They are: spatial agglomeration, untraded as well as market dependencies, small and medium-sized enterprise status, associative or agentic relationships, interaction with large firms inside or outside the cluster and knowledge acquisition, advisory, consultancy and knowledge translation services from research and innovation intermediaries - public and/or private. However, we think their characteristics demand further recognition of the interactive and often innovative communication networks by means of which these cluster incumbents interact globally. This is because they are set within a worldwide system that can be conceptualised as an exemplar of the well-known construct known as an ‘assemblage’ (Deleuze and Guattari, 2004a). Unlike more recent treatments from De Landa (2019) and others, we try to concentrate on the motive power of the ‘agentic’ impulses of ‘desire’ that motivate human action (e.g. regarding ‘God, Gold or Glory’ as commonly-rehearsed motivators for colonialism of various kinds). It has been more common to use ‘assemblage theory’ to analyse the interlocking ‘machinic’ elements of complex systems like power networks or laboratory interactions. To unlock the mysteries of system interlocking in our selected tax havens, which comprise Wilmington, Delaware (US), Ireland (EU) and Gibraltar (former EU, now British Overseas Territory) – post-Brexit - occupying a ‘quantum’ space ‘in which both the colonial and post-colonial find expression’ (Perera, 2021). Methodologically, we seek ‘pattern recognition’ to identify the lineaments that explain these clusters and the ‘agentic’ actors that motivate them.

Two KaiABC systems control circadian oscillations in one cyanobacterium

The circadian clock of cyanobacteria, which predicts daily environmental changes, typically includes a standard oscillator consisting of proteins KaiA, KaiB, and KaiC. However, several cyanobacteria have diverse Kai protein homologs of unclear function. In particular, Synechocystis sp. PCC 6803 harbours, in addition to a canonical kaiABC gene cluster (named kaiAB1C1), two further kaiB and kaiC homologs (kaiB2, kaiB3, kaiC2, kaiC3). Here, we identify a chimeric KaiA homolog, named KaiA3, encoded by a gene located upstream of kaiB3. At the N-terminus, KaiA3 is similar to response-regulator receiver domains, whereas its C-terminal domain resembles that of KaiA. Homology analysis shows that a KaiA3-KaiB3-KaiC3 system exists in several cyanobacteria and other bacteria. Using the Synechocystis sp. PCC 6803 homologs, we observe circadian oscillations in KaiC3 phosphorylation in vitro in the presence of KaiA3 and KaiB3. Mutations of kaiA3 affect KaiC3 phosphorylation, leading to growth defects under both mixotrophic and chemoheterotrophic conditions. KaiC1 and KaiC3 exhibit phase-locked free-running phosphorylation rhythms. Deletion of either system (∆kaiAB1C1 or ∆kaiA3B3C3) alters the period of the cellular backscattering rhythm. Furthermore, both oscillators are required to maintain high-amplitude, self-sustained backscatter oscillations with a period of approximately 24 h, indicating their interconnected nature.

Cosmology with galaxy cluster properties using machine learning

Context. Galaxy clusters are the largest gravitating structures in the universe, and their mass assembly is sensitive to the underlying cosmology. Their mass function, baryon fraction, and mass distribution have been used to infer cosmological parameters despite the presence of systematics. However, the complexity of the scaling relations among galaxy cluster properties has never been fully exploited, limiting their potential as a cosmological probe. Aims. We propose the first machine learning (ML) method using galaxy cluster properties from hydrodynamical simulations in different cosmologies to predict cosmological parameters combining a series of canonical cluster observables, such as gas mass, gas bolometric luminosity, gas temperature, stellar mass, cluster radius, total mass, and velocity dispersion at different redshifts. Methods. The ML model was trained on mock “measurements” of these observable quantities from Magneticum multi-cosmology simulations to derive unbiased constraints on a set of cosmological parameters. These include the mass density parameter, Ωm, the power spectrum normalization, σ8, the baryonic density parameter, Ωb, and the reduced Hubble constant, h0. Results. We tested the ML model on catalogs of a few hundred clusters taken, in turn, from each simulation and found that the ML model can correctly predict the cosmology from where they have been picked. The cumulative accuracy depends on the cosmology, ranging from 21% to 75%. We demonstrate that this is sufficient to derive unbiased constraints on the main cosmological parameters with errors on the order of ~14% for Ωm, ~8% for σ8, ~6% for Ωb, and ~3% for h0. Conclusions. This proof-of-concept analysis, though based on a limited variety of multi-cosmology simulations, shows that ML can efficiently map the correlations in the multidimensional space of the observed quantities to the cosmological parameter space and narrow down the probability that a given sample belongs to a given cosmological parameter combination. More large-volume, mid-resolution, multi-cosmology hydro-simulations need to be produced to expand the applicability to a wider cosmological parameter range. However, this first test is exceptionally promising, as it shows that these ML tools can be applied to cluster samples from multiwavelength observations from surveys such as Rubin/LSST, CSST, Euclid, and Roman in optical and near-infrared bands, and eROSITA in X-rays, to the constrain cosmology and effect of baryonic feedback.

Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s.

During the last few centuries D. melanogaster populations were invaded by several transposable elements, the most recent of which was thought to be the P-element between 1950 and 1980. Here we describe a novel TE, which we named Spoink, that has invaded D. melanogaster. It is a 5216nt LTR retrotransposon of the Ty3/gypsy superfamily. Relying on strains sampled at different times during the last century we show that Spoink invaded worldwide D. melanogaster populations after the P-element between 1983 and 1993. This invasion was likely triggered by a horizontal transfer from the D. willistoni group, much as the P-element. Spoink is probably silenced by the piRNA pathway in natural populations and about 1/3 of the examined strains have an insertion into a canonical piRNA cluster such as 42AB. Given the degree of genetic investigation of D. melanogaster it is perhaps surprising that Spoink was able to invade unnoticed.

Temporal Variations in Plankton Communities and Environmental Factors in the Shipra, a Central Himalayan Tributary of the Kosi River in Uttarakhand, India.

The essential role of smaller streams and tributaries indigenous to the area is crucial in revitalizing and restoring the main river system. The present study unraveled the relationship between plankton communities and environmental variables in the Shipra River, a Central Himalayan tributary of the Kosi River in Uttarakhand, India. Plankton distribution, abundance, and presence were investigated at four locations: upstream (S1 and S2) and downstream (S3 and S4). Forty-eight genera of phytoplankton and zooplankton have been identified belonging to ten classes (Bacillariophyceae, Chlorophyceae, Zygnematophyceae, Cyanophyceae, Euglenopyceae, Protozoa, Rotifers, Copepoda, Cladocera, and Insecta) based on the findings. Winter was dominated by phytoplankton (Navicula spp., Nitzchia spp., Diatom spp.); summer and monsoon by zooplankton (Daphnia spp., Cyclops spp., Keratella spp., Brachionus spp.). Plankton communities of the tributary were assessed using diversity indices (Shannon-Weiner's index (H), Simpson's diversity index (1-D), and Evenness Index (E)). Seasonal variations in water temperature, specific conductivity, total dissolved solids, dissolved oxygen, nitrate, and ammonium ions were found to be statistically significant (p<0.05). Canonical Correspondence Analysis, K-dominance plots, cluster analysis, and NMDS analysis showed the dynamic nature of the plankton communities with seasonal physiochemical variations in the unexplored Himalayan tributary. The plankton communities exhibited significant temporal fluctuations with physicochemical factors.

Water quality assessment in relation to fish assemblage using multivariate analysis in Manasbal Lake, Kashmir

ABSTRACT Water is necessary for the survival of any living being on this planet and in today’s world, it has become a limiting resource because of anthropogenic pressures like pollution, climate change, overexploitation etc. To maintain the water bodies in a proper condition from time to time, analysis of the water quality is highly recommended. So an attempt was made to have a detailed analysis of the surface water quality of the deepest freshwater lake in India, the Manasbal Lake, and to know the impact of these parameters on the distribution of fish fauna in the lake. The different physicochemical aspects of the lake were analyzed spatially and seasonally for a period of two years. The results from the principal component analysis revealed that the main parameters affecting the water quality in Manasbal Lake include total dissolved solids, electrical conductivity, total phosphorus, nitrates, pH, free carbon dioxide, dissolved oxygen and alkalinity. The study also reported a similarity in physicochemical aspects as well as the type of fish fauna from Sites-I and Site-III. Overall the physicochemical aspects were seen to impact the distribution of different fish species in the lake as reported from the canonical correspondence and cluster analysis. pH and nitrates were found to impact the distribution of fish species like Cyprinus carpio, Carassius carassius, Schizothorax niger and S. curvifrons whereas the main parameters affecting the distribution of Pethia conchonius, Crossocheilus diplochilus and Gambusia holbrooki were dissolved oxygen, free carbon dioxide and water temperature. The overall water quality of the lake is good for the proper growth and survival of the fish species and also for domestic purposes. This study will be very helpful to form baseline information for future research, as very scanty information is available related to such work.

APPLICATION OF MULTIVARIATE STATISTICAL ANALYSIS IN CHARACTERISING THE PHENOTYPIC VARIABILITY OF LOCALLY ADAPTED MUSCOVY DUCKS (CAIRINA MOSCHATA) IN NIGERIA

While there are studies that describe the biometric traits and phenotypic variations in Muscovy ducks in Nigeria, there are limited studies that employ a multivariate approach to depict the phenotypic variability of Muscovy ducks in Nigeria. Therefore, this study aimed to explicate genetic variabilities within C. moschata using qualitative and biometric traits. This study used a multivariate statistical method to phenotypically characterise locally adapted Muscovy duck populations from seven ecogeographical locations in Ibadan, Nigeria. Four qualitative traits (eye colour, bill colour, bean colour and shank colour) and eleven biometric traits (head length, neck length, body length, wings length, shank length, toe length, thigh length, bill length, breast length, breast width and bodyweight) were evaluated in 201 ducks (109 males and 92 females). To study the possible effects of geographical locations on selected phenotypes, frequency distribution, univariate analysis, stepwise and canonical discriminant analyses and cluster analysis were performed. The association between body weight (BWT) and other biometric traits was assessed using the Pearson product-moment correlation coefficient. Male ducks (drakes) were generally more abundant than female ducks (hens). The most prevalent colour traits of locally adapted Muscovy ducks were brown eye colour (70.65 %), black bean colour (62.69 %), pinkish white bill colour (45.27 %) and grey shank colour (56.22 %). Overall, ecogeographical location did not significantly affect (p &lt; 0.05) the measured biometric traits. However, across all locations, the sexual dimorphism was favourable in male ducks, with respect to biometric traits. Stepwise-canonical discriminant analysis revealed a substantial intermixing of biometric traits, especially in Molete, Oje, Adogba and Ajibode ducks. Similarly, the cluster analysis, although it separated the birds into different clusters, showed some level of admixture. The small Mahalanobis distance (0.61 − 3.88) suggested that, with respect to location, there was more morphological similarity than dissimilarity between ducks. The correlation analysis revealed that the body weight of ducks can be fairly estimated from other biometric traits due to their positive, statistically significant correlation. In general, the ducks from all seven ecogeographical locations were rather homogeneous than heterogeneous.

Evolution of primate interferon-induced transmembrane proteins (IFITMs): a story of gain and loss with a differentiation into a canonical cluster and IFITM retrogenes.

Interferon-inducible transmembrane proteins (IFITMs) are a family of transmembrane proteins. The subgroup of immunity-related (IR-)IFITMs is involved in adaptive and innate immune responses, being especially active against viruses. Here, we suggest that IFITMs should be classified as (1) a canonical IFITM gene cluster, which is located on the same chromosome, and (2) IFITM retrogenes, with a random and unique location at different positions within the genome. Phylogenetic analyses of the canonical cluster revealed the existence of three novel groups of primate IFITMs (pIFITM) in the IR-IFITM clade: the prosimian pIFITMs(pro), the new world monkey pIFITMs(nwm) and the old world monkey pIFITMs(owm). Therefore, we propose a new nomenclature: IR-pIFITM1, IR-pIFITM2, IR-pIFITM3, IR-pIFITMnwm, IR-pIFITMowm, and IR-pIFITMpro. We observed divergent evolution for pIFITM5 and pIFITM10, and evidence for concerted evolution and a mechanism of birth-and-death evolution model for the IR-pIFITMs. In contrast, the IFITMs scattered throughout the genomes possessed features of retrogenes retrotransposed by class 1 transposable elements. The origin of the IFITM retrogenes correspond to more recent events. We hypothesize that the transcript of a canonical IFITM3 has been constantly retrotransposed using class 1 transposable elements resulting in the IFITM retro(pseudo)genes. The unique pattern of each species has most likely been caused by constant pseudogenization and loss of the retro(pseudo)genes. This suggests a third mechanism of evolution for the IR-IFITMs in primates, similar to the birth-and-death model of evolution, but via a transposable element mechanism, which resulted in retro(pseudo)genes.

Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas.

Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and diverse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.

Canonical Monte Carlo multispin cluster method

We present a new Canonical Multispin-flip Cluster Monte Carlo algorithm for Ising model and describe efficient implementations for hybrid supercomputer. Our method takes advantage of the computing architecture for parallel and multi-threaded operations and uses a sequential cluster state update scheme. Due to the peculiarity of the implementation, the method is more effective for models with a restricted radius of interaction. It is based on combining a random selection of spin cluster by the Monte Carlo method with a complete enumeration of the all states of the selected cluster. To show how it works we applied our method to models of interacting magnetic Ising-moments: ferromagnetic Ising model, the Edwards–Anderson spin glass model, dipolar spin ice on hexagonal and pentagonal Cairo lattices.

Noncanonical vortex states and dynamics in Bose-Einstein condensates

Vortex excitations triggered by nonlinear interactions in Bose-Einstein condensates have attracted interest in the study of ultracold atoms. However, most studies focus on canonical vortex states with integer topological charges. In this paper, we study the dynamic properties of noncanonical vortex condensates with three phase distributions: power-exponent, new type power-exponent and oscillation type. The results show that the noncanonical vortices are dynamic unstable and their density distributions obviously depend on the phase parameters of the initial optical phase masks. Different noncanonical vortices decay into canonical clusters with diverse configurations showing rich topological excitation patterns. In particular, a new power exponential noncanonical vortex state decays into a stable canonical polygonal vortex cluster structure. Because the phase structures of the noncanonical optical vortices destroy the rotational symmetry of the condensate, the angular momentum of the condensate is no longer quantized, and its value changes with the power of the azimuthal angle of the optical field or the oscillation frequency, which is obviously different from the evolution of the corresponding noncanonical vortex optical field itself. In the dynamical process, the center-of-mass trajectory of noncanonical vortex condensates with the new type of power exponent phase is always a point, while for the noncanonical vortex condensates with power exponent and oscillating phase, the center-of-mass trajectories are ellipses centering at the origin of coordinates.

Tau‐Neurodegeneration mismatch reveals vulnerability and resilience in Alzheimer’s continuum and Non‐Alzheimer’s pathophysiology

AbstractBackgroundIn previous work (Das et al., 2021), we exploited the non‐specific nature of neurodegeneration by investigating the amount and spatial pattern of deviation from the level of neurodegeneration (N) expected for a given level of tau (T). Using a data‐driven clustering approach based on T‐N mismatch, we found phenotypes that had greater N than expected for T (“vulnerable”) and phenotypes with less N than expected for T (“resilient”) in specific patterns. Here we extend this work to include amyloid positive (A+) and negative (A‐) participants. The logic of inclusion of A‐ individuals is that areas of mismatch in A+ individuals is likely driven by factors outside of AD pathology, which can be present in the absence of AD pathology.MethodWe employed cortical thickness to represent N and 18F‐flortaucipir tracer uptake as T for 104 bilateral cortical regions of interest (ROI) in 343 symptomatic individuals including both A+ and A‐ from ADNI. We established T‐N robust regression and partitioned participants based on thresholded residuals. Longitudinal trajectories of cognitive scores were assessed with linear mixed‐effects model effect models using CDRSB as the dependent variable.ResultWe replicated prior work and obtained clusters with distinct T‐N mismatch patterns. We defined the largest group as “canonical”, as it displayed typical T‐N relationships (N∼T, low residuals). The limbic vulnerable cluster displayed N&gt;T (negative residuals) in limbic regions, while diffuse vulnerable group displayed N&gt;T throughout the cortex. Alternatively, the resilient (N&lt;T, positive residuals) clusters were classified as limbic resilient or prefrontal resilient based on the pattern of this relationship. Note the highly similar regional patterns of the A+ and A‐ subgroups, supporting our hypothesis that this residual reflects non‐AD related phenomenology which could be present irrespective of amyloid status. Phenotypes differed in longitudinal cognitive trajectories. The vulnerable clusters declined significantly faster than the canonical cluster regardless of amyloid status likely attributable to the presence of non‐AD pathologies. The resilient groups tended to progress less than the canonical group.ConclusionOur findings suggest T‐N mismatch depicts vulnerability and resilience likely attributable to non‐AD factors. This may provide an approach for detecting co‐pathologies in AD continuum and benefiting therapeutic management.

Chemosensory pathways of Halomonas titanicae KHS3 control chemotaxis behaviour and biofilm formation.

Halomonas titanicae KHS3 is a marine bacterium whose genome codes for two different chemosensory pathways. Chemosensory gene cluster 1 is very similar to the canonical Che cluster from Escherichia coli. Chemosensory cluster 2 includes a gene coding for a diguanylate cyclase with receiver domains, suggesting that it belongs to the functional group that regulates alternative cellular functions other than chemotaxis. In this work we assess the functional roles of both chemosensory pathways through approaches that include the heterologous expression of Halomonas proteins in E. coli strains and phenotypic analyses of Halomonas mutants. Our results confirm that chemosensory cluster 1 is indeed involved in chemotaxis behaviour, and only proteins from this cluster complement E. coli defects. We present evidence suggesting that chemosensory cluster 2 resembles the Wsp pathway from Pseudomonas, since the corresponding methylesterase mutant shows an increased methylation level of the cognate receptor and develops a wrinkly colony morphology correlated with an increased ability to form biofilm. Consistently, mutational interruption of this gene cluster correlates with low levels of biofilm. Our results suggest that the proteins from each pathway assemble and function independently. However, the phenotypic characteristics of the mutants show functional connections between the pathways controlled by each chemosensory system.

Changes in soil chemical properties and plant species composition during primary succession on an oceanic island

AbstractQuestionsWhat is the influence of time and environmental factors such as climate and topography on soil chemical properties and composition of vascular plants during primary succession on lava flows of an oceanic island? How is compositional change characterized and which successional stages can be distinguished?LocationLa Palma, Canary Islands.MethodsWe sampled soil properties and vascular plants in 72 plots on a long‐term chronosequence of 10 lava flows ranging in age between 40 and over 20,000 years in the semi‐arid lowlands of La Palma Island. Soil properties were analyzed by general least‐squares models (GLS), while canonical correspondence analysis (CCA), cluster analysis and multiresponse permutation procedures (MRPP) were applied to investigate compositional change.ResultsSoil characteristics and plant species composition during primary succession were strongly affected by substrate age but also by climatic and topographic factors. Values of most soil properties increased with lava flow age, while pH decreased. Soil organic matter, phosphorus, exchangeable calcium and ammonium revealed a positive correlation with mean annual precipitation. Lava flow age was always the most important independent factor determining plant assembly followed by mean annual precipitation. Four successional stages and their composition of indicator species, life strategies and species status could be defined. Alien species did not alter successional trajectories.ConclusionTime, climate and topography simultaneously affect soil properties and plant composition during primary succession on lava flows. The climatic windward–leeward gradient on La Palma Island influences plant colonization and soil development in the semi‐arid coastal areas. Favorable conditions (moisture) can speed up primary succession. Compositional changes suggest convergence during primary succession. During the entire colonization process, dominant successional shrubs are endemics, highlighting the importance of evolutionary adaptation to volcanic disturbances.

A Paradise for Rare Species: Tanaidacean Fauna of the West African Continental Margin

The benthic ecology of the Gulf of Guinea is critically understudied, and knowledge about the composition and biodiversity of the tanaidacean communities remains lacking. Our analysis of tanaidacean collection from 270 quantitative samples collected using 0.1 m2van Veen grab along the Ghanaian coast (nine transects, six stations at each transect, 25–1,000 m depth range) reveals a high species richness and very low abundance. The mean density of Tanaidacea across all the samples equals only 0.03 ± 0.55 ind./0.1 m2. A total of 87 tanaidacean species were recorded, of which only three were known for science (3.4%), emphasizing the need for intensified taxonomic effort in this region.Circa40% of the species were singletons, 98% of the species had a total abundance lower than 10 individuals, and approximately half of the species were found only in one sample. The highest species richness was recorded in the slope (500–1,000 m), despite the elevated levels of barium and hydrocarbons at those depths. This area was also characterized by the most unique species composition. Species accumulation curves did not reach an asymptote, suggesting an undersampling of the area and a great rarity of the species. Results of the canonical correspondence analysis (CCA) and cluster analysis demonstrated a positive influence of oxygen concentration and fluorescence, particularly in the shallow shelf sites (25–50 m), which were characterized by a higher abundance of Tanaidacea. Depth zonation of tanaidacean communities with a division between shallow-water taxa (Leptocheliidae Lang, 1973 and Kalliapseudidae Lang, 1956) through families with wide bathymetric range (Pseudotanaidae Sieg, 1976, Apseudidae Leach, 1814) to the true deep-sea forms (Paranarthrurellidae Błażewicz, Jóźwiak and Frutos, 2019) is also evident. We further discuss the problems associated with multivariate analysis of highly speciose but less abundant taxa.

Environmental and human risk assessment of heavy metals at northern Nile Delta region using geostatistical analyses

Present study aims to assess the possible toxic metal hazard of Pb, Cd and Fe in street dust and soil on environment and human health at the northern Deltaic region of Egypt using spatial and statistical analyses. To achieve this aim, 13 different sites were sampled for street dust and soil to represent various residential, industrial and agricultural activities. Unsupervised classification of multispectral Landsat OLI image (March 2021) helped to identify the sampling sites. Heavy metals were evaluated using environmental and human health risk indices incorporated in a GIS environment through geostatistical techniques. Multivariate analyses were demonstrated for further interpretation including principle components analysis (PCA), Canonical correlation analysis (CCA) and cluster analysis (CA). The average metal concentrations in street dust for Pb, Cd and Fe were 0.57, 0.07 and 435.92 mg/kg, however in soil were 0.61, 0.08 and 1098.30 mg/kg, respectively. The mean value of Cd and Pb in soil was higher than street dust while the reverse was reported for Fe. Spatial distribution maps showed that the high levels of metals in street dust were observed in the southern parts of the study area due to industrial activities and automobile emissions. The risk assessment exhibited that the area suffers from serious metals pollution particularly Cd. Human risk assessment indicated that derma is the main exposure route that harmfully affects the human health. Exposure to the pollutant through the three pathways is higher for Pb than Cd. The values of hazard quotient (HQ) followed the next trend; Fe > Pb > Cd. The measured cancer risk was negligible in the investigated area. Statistical analysis of PCA and CCA showed that industrial and agricultural activities contribute to the occurrence of heavy metals.

Application of multivariate statistical analysis in ecological environment research

Multivariate statistics has proven many outstanding advantages and has been used extensively in various studies in the ecological environment field. They supported ecologists to discover the structure and previous relatively objective summary of the primary features of the data. In this paper, some important statistical techniques, including principal component analysis (PCA), canonical correspondence analysis (CCA) and cluster analysis, are explained briefly. Each of them is also examined by a corresponding case-study. The PCA is applied to identify and analyze the relationship between mangrove plant communities and soil factors. Meanwhile, the CCA is put in an application to analyze the relationship between the two sets of species and soil data, from which to determine the effect of soil on the distribution of dominant species. Finally, cluster analysis is examined to analyze the similarities among species in the studied area.

Assessment of temperature effects on body shape in Nile tilapia, Oreochromis niloticus juveniles using the truss network system

Among the environmental factors, water temperature has a significant effect on many aspects of fish life. This study was carried out to examine effects of water temperature on body shape of Nile tilapia, Oreochromis niloticus during the early stages of life using truss network system. A total of 150 newly-born fry were reared in three temperature treatments (22, 28 and 34°C) for 40 days. At the end of experiment, the left side of the specimens was photographed. To achieve the body shape data, 13 landmark-points were digitized using tpsDig2 software. The extracted data were justified with generalized procrustes analysis, then the differences of body shape among groups were investigated using the principal component analysis (PCA), canonical variate analysis (CVA) and cluster analysis (CA). There were significant differences in body shape of the treatments. The results of CVA and CA indicated that one of the important factors in the aquatic habitats is water temperature that influences the body shape of the Nile tilapia during the first stages (larval and juvenile stages) of growth.

Quantum Chemical Study of a Radical Relay Mechanism for the HydG-Catalyzed Synthesis of a Fe(II)(CO)2(CN)cysteine Precursor to the H-Cluster of [FeFe] Hydrogenase.

The [FeFe] hydrogenase catalyzes the redox interconversion of protons and H2 with a Fe-S "H-cluster" employing CO, CN, and azadithiolate ligands to two Fe centers. The biosynthesis of the H-cluster is a highly interesting reaction carried out by a set of Fe-S maturase enzymes called HydE, HydF, and HydG. HydG, a member of the radical S-adenosylmethionine (rSAM) family, converts tyrosine, cysteine, and Fe(II) into an organometallic Fe(II)(CO)2(CN)cysteine "synthon", which serves as the substrate for HydE. Although key aspects of the HydG mechanism have been experimentally determined via isotope-sensitive spectroscopic methods, other important mechanistic questions have eluded experimental determination. Here, we use computational quantum chemistry to refine the mechanism of the HydG catalytic reaction. We utilize quantum mechanics/molecular mechanics simulations to investigate the reactions at the canonical Fe-S cluster, where a radical cleavage of the tyrosine substrate takes place and proceeds through a relay of radical intermediates to form HCN and a COO•- radical anion. We then carry out a broken-symmetry density functional theory study of the reactions at the unusual five-iron auxiliary Fe-S cluster, where two equivalents of CN- and COOH• coordinate to the fifth "dangler iron" in a series of substitution and redox reactions that yield the synthon as the final product for further processing by HydE.