Non-random Distribution Research Articles

Non-Random Distribution of Boreus hyemalis Among Bryophyte Hosts: Evidence from Field and Laboratory Tests.

Our understanding of herbivorous insect's host selection is often based on observed associations with host plants, which can be biased by relative plant abundance, leading to inaccurate assumptions of preference. These biases may be particularly pronounced for insects associated with bryophytes, where dominance patterns are less evident. Estimating selection tendencies is also challenging for rare species with unique ecologies. Boreus hyemalis, a winter-active insect, associates with a range of bryophyte species, yet its specificity in moss-host selection remains unclear. This study investigates whether B. hyemalis shows non-random distribution among bryophyte species in natural habitats and laboratory settings. Field surveys revealed associations with 21 moss species, with significant selection tendencies toward Dicranella heteromalla and Hypnum cupressiforme, with moss species richness being a key factor for boreid inhabitance. Laboratory tests assessed selection among 14 moss species, including H. cupressiforme morphotypes, under controlled conditions. Results indicated Polytrichum formosum was the most frequently selected in the lab. Despite some discrepancies between field and lab findings, B. hyemalis shows specific selection tendencies for particular moss species. These results provide new insights into the ecological interactions between bryophytes and this winter-active insect, emphasizing the importance of moss structure and species richness in shaping B. hyemalis distribution.

Strong convergence of the empirical spectral distribution of a unified matrix model

Let [Formula: see text] is a positive definite matrix and [Formula: see text] with [Formula: see text] being independent and identically distributed (i.i.d.) centered real random variables. Consider the matrix [Formula: see text] where [Formula: see text] and [Formula: see text] are two projection matrices (deterministic or random) satisfying [Formula: see text] and [Formula: see text]. Additionally, if [Formula: see text] and [Formula: see text] are random matrices, they are independent of [Formula: see text]. In this paper, we demonstrate that the empirical spectral distribution of [Formula: see text] converges almost surely to a non-random distribution when [Formula: see text] and [Formula: see text], assuming [Formula: see text] has finite second moment.

Comparison of the Distribution Patterns of Microsatellites Across the Genomes of Reptiles.

Microsatellites or simple sequence repeats (SSRs) are prevalent across various organisms' genomes. However, their distribution patterns and evolutionary dynamics in reptile genomes are rarely studied systematically. We herein conducted a comprehensive analysis of SSRs in the genomes of 36 reptile species. Our findings revealed that the total number of SSRs ranged from 1,840,965 to 7,664,452, accounting for 2.16%-8.19% of the genomes analyzed. The relative density ranged from 21,567.82 to 81,889.41 bp per megabase (Mbp). The abundance of different SSR categories followed the pattern of imperfect SSR (I-SSR) > perfect SSR (P-SSR) > compound SSR (C-SSR). A significant positive correlation was observed between the number of SSRs and genome size (p = 0.0034), whereas SSR frequency (p = 0.013) or density (p = 0.0099) showed a negative correlation with genome size. Furthermore, no correlation was found between SSR length and genome size. Mononucleotide repeats were the most common P-SSRs in crocodilians and turtles, whereas mononucleotides, trinucleotides, or tetranucleotides were the most common P-SSRs in snakes, lizards, and tuatara. P-SSRs of varying motif sizes showed nonrandom distribution across different genic regions, with AT-rich repeats being predominant. The genomic SSR content of the squamate lineage ranked the highest in abundance and variability, whereas crocodilians and turtles showed a slowly evolving and reduced microsatellite landscape. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that genes harboring P-SSRs in the coding DNA sequence regions were primarily involved in the regulation of transcription and translation processes. The SSR dataset generated in this study provides potential candidates for functional analysis and calls for broader-scale analyses across the evolutionary spectrum.

Your room is ready: Tourism and urban revival

Tourism is an essential sector of the global economy, contributing significantly to GDP and employment. Despite its importance, our understanding of its impact on urban economic activity remains limited. This paper aims to fill this gap by examining the impact of tourism on urban transformation using a dataset of hotel openings in Madrid from 2001–2010. I show that hotel openings positively impact the number of establishments and employment by using the number of protected buildings as an instrumental variable to account for the non-random distribution of hotel openings. Interestingly, hotel openings contribute to changes in the composition of the economic activities and the business structures, enhancing tourist-oriented corporate-owned businesses over other individual-owned companies. Finally, economic effects extend to the real estate market, increasing rental prices and residential investment.

Reindeer carcasses modulate vegetation composition and greenness in High-Arctic tundra.

Vertebrate carrion is an integral part of foodwebs in ecosystems and can impact biodiversity at the local as well as the landscape scale. However, very little knowledge currently exists about the ecological role of carrion in the Arctic ecosystems. We conducted a ground survey on the cover of five plant functional groups at paired reindeer carcass and control sites and analysed the relationship between cover and carcass presence in the Arctic tundra of Svalbard. Vegetation indices from Red-Green-Blue (RGB) imagery captured by drones complemented this, assessing plant productivity in terms of ‘spectral greening’ and modelling the relationship between vegetation index values and carcass distance. We show that graminoids capitalised most from carcass presence, whereas bryophytes and lichen showed decreases in cover. Woody plant and forb covers were not significantly impacted by carcass presence. The Red Green Blue Vegetation Index decreased locally at fresh carcasses (i.e. <1 year old) but showed an increase at more established carcass sites (i.e. >1 year). We show that carcasses have differential impacts on the plant functional groups of Svalbard’s tundra and induce a local ‘green-up’ through secondary succession within 2 metres of the carcass. Given their non-random distribution, carcasses may contribute to vegetation heterogeneity at landscape scales. This is relevant for understanding how climate change-induced reindeer mortalities will impact tundra plant community composition in the future.

The dynamics of protest participation patterns: analysis of the Polish case

ABSTRACT A variety of research techniques, including survey research, are used to estimate the participation turnout in nonviolent protests. The issues with survey data interpretation, as well as any discrepancies and emerging research methodologies, are illustrated using Poland as an example. The problems of comparison and measurement that have been identified include: (1) non-random distribution of activism in the population, (2) variability of the pattern over time (dynamics of contention), and (3) sampling and format of questions in surveys. A comparison with the protest cultures of other European countries highlights that Poland has some of the lowest average values of declared engagement in demonstrations. However, it also points to a significant dynamic increase in 2022 and differences in declaration levels during the studied period (2006–2022). The obtained results based on Polish national survey (CBOS) and European Social Survey indicate a rising trend in recent years in Poland, with a straightforward estimation suggesting an annual average participation of around 1.8 million adult citizens in street demonstrations from 2016 to 2022. Research conducted within the ESS indicates higher values for the same period, at around 2.6 million.

Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions

Microbes in the dark oceans are a key determinant of remineralization of sinking carbon particles. However, most marine ecosystem models overlook how microbes aggregate on particles and the microscale interactions between particle-associated microbes, making it difficult to obtain mechanistic insights on their vertical power-law decay pattern. Here, we present a spatial population model where the attachment and detachment processes of bacterial cells depend on local density of particle-associated bacteria. We show that the power-law relationship can emerge when the non-random aggregated distribution of bacteria is considered without any depth-specific environmental parameters. Furthermore, the comparison between model behavior and empirical patterns in the Pacific and Southern Ocean indicated that temperature-dependent hydrolysis rate and nutrient-dependent sinking rate of particles are key parameters to explain the regional variations of the power-law exponent. The mechanistic approach developed here provides a pathway to link micro-scale interactions between individuals to macro-scale food chain structures and carbon cycle.

Non-random distribution of Plasmodium Species infections and associated clinical features in children in the lake Victoria region, Kenya, 2012–2018

BackgroundWhile Plasmodium falciparum (Pf) stands out as the most lethal malaria parasite species in humans, the impact of other species should not be dismissed. Moreover, there is a notable lack of understanding of mixed-species infections and their clinical implications.MethodsWe conducted eight school-based cross-sectional malariometric surveys in the Lake Victoria region of western Kenya between January–February 2012 and September–October 2018. In each survey, a minimum of 100 children aged 3 to 15 years were randomly chosen from a school in Ungoye village on the mainland and as well as from each school selected in every catchment area on Mfangano island. Plasmodium infection was determined by microscopy and nested polymerase chain reaction (PCR). The multiple-kind lottery (MKL) model calculated the expected distribution of Plasmodium infections in the population and compared it to observed values using a chi-squared test (χ2).ResultsThe Plasmodium prevalence was 25.9% (2521/9724) by microscopy and 51.1% (4969/9724) by PCR. Among all infections detected by PCR, Pf, P. malariae (Pm), and P. ovale (Po) mono-infections were 58.6%, 3.1%, and 1.8%, respectively. Pf/Pm, Pf/Po, Pm/Po, and Pf/Pm/Po co-infections were 23.5%, 4.3%, 0.1%, and 8.6%, respectively. MKL modelling revealed non-random distributions, with frequencies of Pf/Pm and Pf/Pm/Po co-infections being significantly higher than expected (χ2 = 3385.60, p < 0.001). Pf co-infections with Pm and Po were associated with a decreased risk of fever (aOR 0.64, 95% CI 0.46–0.83; p = 0.01) and increased risks of splenomegaly (aOR 12.79, 95% CI 9.69–16.9; p < 0.001) and anaemia (aOR 2.57, 95% CI 2.09–3.15; p < 0.001), compared to single-species infections.ConclusionThis study sheds light on the potential interaction between Pf and Pm and/or Po. Given the clinical significance of mixed-species infections, improved diagnostics, and case management of Pm and Po are urgently needed.

Harmonic Wavelet Neural Network for Discovering Neuropathological Propagation Patterns in Alzheimer's Disease.

Emerging research indicates that the degenerative biomarkers associated with Alzheimer's disease (AD) exhibit a non-random distribution within the cerebral cortex, instead following the structural brain network. The alterations in brain networks occur much earlier than the onset of clinical symptoms, thereby affecting the progression of brain disease. In this context, the utilization of computational methods to ascertain the propagation patterns of neuropathological events would contribute to the comprehension of the pathophysiological mechanism involved in the evolution of AD. Despite the encouraging findings achieved by existing graph-based deep learning approaches in analyzing irregular graph data, their applications in identifying the spreading pathway of neuropathology are limited due to two disadvantages. They include (1) lack of a common brain network as an unbiased reference basis for group comparison, and (2) lack of an appropriate mechanism for the identification of propagation patterns. To this end, we propose a proof-of-concept harmonic wavelet neural network (HWNN) to predict the early stage of AD and localize disease-related significant wavelets, which can be used to characterize the spreading pathways of neuropathological events across the brain network. The extensive experiments constructed on both synthetic and real datasets demonstrate that our proposed method achieves superior performance in classification accuracy and statistical power of identifying propagation patterns, compared with other representative approaches.

Characterization of G-quadruplexes in the Helicobacter pylori genome and assessment of therapeutic potential of G4 ligands.

Helicobacter pylori, a leading human pathogen associated with duodenal ulcer and gastric cancer, presents a significant threat to human health due to increasing antibiotic resistance rates. This study investigates G-quadruplexes (G4s), which are non-canonical secondary structures form in G-rich regions within the H. pylori genome. Extensive research on G4s in eukaryotes has revealed their role in epigenetically regulating cellular processes like gene transcription, DNA replication, and oncogene expression. However, understanding of G4-mediated gene regulation in other organisms, especially bacterial pathogens, remains limited. Although G4 motifs have been extensively studied in a few bacterial species such as Mycobacterium, Streptococci, and Helicobacter, research on G4 motifs in other bacterial species is still sparse. Like in other organisms such as archaea, mammals, and viruses, G4s in H. pylori display a non-random distribution primarily situated within open reading frames of various protein-coding genes. The occurrence of G4s in functional regions of the genome and their conservation across different species indicates that their placement is not random, suggesting an evolutionary pressure to maintain these sequences at specific genomic sites. Moreover, G-quadruplexes show enrichment in specific gene classes, suggesting their potential involvement in regulating the expression of genes related to cell wall/membrane/envelope biogenesis, amino acid transport, and metabolism. This indicates a probable regulatory role for G4s in controlling the expression of genes essential for H. pylori survival and virulence. Biophysical techniques such as Circular Dichroism spectroscopy and Nuclear Magnetic Resonance were used to characterize G4 motifs within selected H. pylori genes. The study revealed that G-quadruplex ligand inhibited the growth of H. pylori, with minimal inhibitory concentrations in the low micromolar range. This suggests that targeting G4 structures could offer a promising approach for developing novel anti-H. pylori drugs.

A Descriptive Analysis of Childhood Lead Poisoning in Jefferson County, Kentucky – Louisville’s Silent Epidemic

Introduction In this study we provide an epidemiological description of Elevated Blood Lead Levels (EBLLs) in the pediatric population of Jefferson County, KY. To provide a more thorough epidemiological description of this issue, we put together the largest known pediatric blood lead dataset for Jefferson County and evaluated the data using the Center for Disease Control and Prevention’s current Blood Lead Referent Value (BLRV) of &gt; 3.5 mcg/dL. Methods We collected 111,065 rows of pediatric blood lead data from the Louisville Metro Department of Public Health and Wellness. Descriptive and inferential statistics were used to explore the magnitude of this issue. Unadjusted Risk Ratios (RR) were also calculated by specific demographics. Geographic cluster analysis was produced by the Kulldorff spatial scan statistic. Results There are 74,014 unique children in the blood lead dataset, of which 9,823 had at least one blood lead test &gt; 3.5 mcg/dL. Black children had a 77% increased risk for an EBLL compared to white children (Unadjusted Risk Ratio: 1.77; 95% CI: 1.61, 1.95). Additionally, children who live in the northwest corner of Jefferson County, have an estimated 9.37-fold increased risk for an EBLL compared to children who live elsewhere in the county. Discussion The non-random distribution of EBLLs in Jefferson County is likely due to the distribution of Pre-1950 housing which is a known risk factor for remnant environmental lead. This issue may be a consequence of the systematic financial disinvestment of these neighborhoods via redlining during the 20th century. Childhood lead poisoning remains a critical public health issue in Jefferson County, KY.

Unveiling nuclear chromatin distribution using IsoConcentraChromJ: A flourescence imaging plugin for IsoRegional and IsoVolumetric based ratios analysis.

Chromatin exhibits non-random distribution within the nucleus being arranged into discrete domains that are spatially organized throughout the nuclear space. Both the spatial distribution and structural rearrangement of chromatin domains in the nucleus depend on epigenetic modifications of DNA and/or histones and structural elements such as the nuclear envelope. These components collectively contribute to the organization and rearrangement of chromatin domains, thereby influencing genome architecture and functional regulation. This study develops an innovative, user-friendly, ImageJ-based plugin, called IsoConcentraChromJ, aimed quantitatively delineating the spatial distribution of chromatin regions in concentric patterns. The IsoConcentraChromJ can be applied to quantitative chromatin analysis in both two- and three-dimensional spaces. After DNA and histone staining with fluorescent probes, high-resolution images of nuclei have been obtained using advanced fluorescence microscopy approaches, including confocal and stimulated emission depletion (STED) microscopy. IsoConcentraChromJ workflow comprises the following sequential steps: nucleus segmentation, thresholding, masking, normalization, and trisection with specified ratios for either 2D or 3D acquisitions. The effectiveness of the IsoConcentraChromJ has been validated and demonstrated using experimental datasets consisting in nuclei images of pre-adipocytes and mature adipocytes, encompassing both 2D and 3D imaging. The outcomes allow to characterize the nuclear architecture by calculating the ratios between specific concentric nuclear areas/volumes of acetylated chromatin with respect to total acetylated chromatin and/or total DNA. The novel IsoConcentrapChromJ plugin could represent a valuable resource for researchers investigating the rearrangement of chromatin architecture driven by epigenetic mechanisms using nuclear images obtained by different fluorescence microscopy methods.

Prevalence, intensity, and attachment sites of larval mites (Acari: Erythraeidae) infesting Erginulus clavotibialis, a Neotropical harvestman (Opiliones: Cosmetidae) from Belize

Larval erythraeid mites of the genus Leptus Latreille, 1796 are common ectoparasites of terrestrial arthropods, including harvestmen (Order Opiliones). In this study, we investigated sexual, ontogenetic, and geographic variation in infestations of the Neotropical cosmetid harvestmen Erginulus clavotibialis (Cambridge, 1904) by larval mites across multiple sampling locations in Belize. We did not observe any significant differences in the prevalence or intensity of mite infestation with respect to sex of the host or between juveniles and adults. However, there was significant variation in the prevalence of infestation between field sites, varying from 18-71%. The overall mean intensity of infestation was 3.2 mites/host. Larval mites exhibited a non-random distribution with respect to attachment sites, with significantly more mites occurring on femur IV. Larval mites were absent from the tarsi of the walking legs and were rarely observed attached to the pedipalps or chelicerae of the harvestmen. Of the ten mites attached to hosts that were examined with SEM, six larvae were found in close association to abandoned attachment cones.

Abstract B009: Exploring the putative Kras-p53 mutational interface for vulnerability

Abstract Introduction: Kras Gain of Function mutations are frequently detected in lung, colorectal and pancreatic cancers, in addition to others. Activating Kras mutations results in a constantly active protein, which we reasoned is quite unphysiological, yet it is tolerated by cells since this mutation is seen in hyperplasia. Activating this oncogene is insufficient alone for malignant transformation. Mutations in the tumor suppressor gene (TSG) p53 (the most frequently mutated gene in human cancer), cooperate with mutant Kras and is sufficient to permit full display of the actions of oncogenic Ras (as confirmed in Genetically Engineered Mouse Models and in clinical cases). The phenomenon of oncogene addiction may in fact be the result of obligatory requirements (cellular metabolism or otherwise) brought on by the constant oncogene signaling. This required adjustment in cellular circuitry can be afforded by specific cooperating TSG and since it too is a DNA constant change, becomes an new rigid reality for a cell with a given set of oncogene-TSG pair. p53 mutational spectrum was described as ‘enigmatic’ presumably because they almost never completely abrogate the function of this major regulator suggesting to us a possible essential mechanistic role for the retained transcriptional targets within the (well annotated) p53 transcriptional network. This could represent a putative synthetic lethality opportunity against activated Kras, an oncogene that has proven difficult to drug. We hypothesized that specific mutations in p53 with their respective transcriptional lesions cooperate with unique mutant Kras in tissue specific manner identifying a short list of gene targets for synthetic lethality experiments. Methods: To examine this hypothesis, we analyzed the TCGA database to determine a conserved pair cooperation between common Kras 12C; D or V and the top 6 reported p53 (hot spot) mutations [on residues 175; 245;248;249;273 and 282] in a stage-agnostic manner. To examine whether those putative interactions are cell-type specific, we performed this analysis in 3 different histologies (lung, colon, and pancreas). Results: The results suggested a non-random distribution of p53 mutants among the Kras driven cancers. KRAS (12 C, 12 V, 12 D were reported in 80% of Colon, Pancreas, and Lung Cancer. p53 (175 - 30%) (245 - 30%) (248 - 15%) (249 - 12%) (273 - 6.5%) (282 - 6.5%). More detailed analysis is planned for the poster session. Conclusion: Despite having a single activated oncogene, the distribution of the cooperating p53 mutations is nonrandom so examining the transcriptionally retained gene list represents a novel approach to explore for gene editing experiments. This provides and approach to drug the addiction of cancers to their oncogenes in a cancer specific, and occasionally to target essential proto-oncogene such as Myc where direct inhibition is highly undesirable due to its physiologic roles. Citation Format: Nishanth Thalambedu, Shallya Anand, Haya Safar, Farah Mazahreh, Ahmad Mazin M. Safar. Exploring the putative Kras-p53 mutational interface for vulnerability [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B009.

Are Selenides the Same as Sulfides? Structure, Spectroscopy, and Properties of Narrow-Gap Rare-Earth Semiconductors RE2Sn(S1-xSex)5 (RE = La, Ce; x = 0-0.8).

The ternary rare-earth sulfides RE2SnS5 (RE = La-Nd) and the partial solid solutions RE2Sn(S1-xSex)5 (RE = La, Ce; x = 0-0.8) were prepared in the form of polycrystalline samples by reaction of the elements at 900 °C and as single crystals in the presence of KBr flux. They adopt the La2SnS5-type structure (orthorhombic, space group Pbam, Z = 2) consisting of chains of edge-sharing SnCh6 octahedra separated by RE atoms. Although the cell parameters evolve smoothly in RE2Sn(S1-xSex)5, detailed structural analysis by single-crystal X-ray diffraction revealed a pronounced preference for the Se atoms to occupy two out of the three chalcogen sites, which offers a rationalization for why the all-selenide end-members RE2SnSe5 do not form. Solid-state 119Sn NMR spectra confirmed the nonrandom distribution of SnS6-nSen local environments, which could be resolved into individual resonances. The Raman spectra of RE2SnS5 compounds show an intense peak at 307-320 cm-1 assigned to a symmetric A1g mode, which is dominated by Sn-S bonds; the Raman peak intensities varied with Se substitution in La2Sn(S1-xSex)5. Optical diffuse reflectance spectra, band structure calculations, and electrochemical impedance spectra indicated that these compounds are narrow band gap semiconductors; the optical band gaps are insensitive to RE substitution in RE2SnS5 (0.7 eV) but they gradually decrease with greater Se substitution in RE2Sn(S1-xSex)5 (0.7-0.4 eV).

UV damage induces production of mitochondrial DNA fragments with specific length profiles.

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.

Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana)

The nonrandom distribution of chromosomal characteristics and functional elements—genomic architecture—impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure—ordination, clustering, and phylogenetic methods—we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.

Nestedness of benthic diatom metacommunity in relation to species niche width and environmental variables in a large near-natural catchment

Insight into the non-random distribution patterns of species in different regions is a foundational aim of research in community ecology and biogeography. The nestedness pattern, which investigates changes in species composition and abundance, has been widely used in numerous studies. However, studies on the nestedness of benthic diatoms are extremely rare, and consequently little has been mentioned of their assemblage mechanisms. To fill this gap, based on 168 benthic diatom species from 147 sampling sites in the Thousand Island Lake (TIL) catchment, we calculated their nestedness and niche width with the aim of i) analyzing the nestedness of benthic diatoms communities with different attachment abilities in TIL; ii) calculating niche width differences between nested and idiosyncratic species with different attachment abilities; iii) investigating the differences in alpha and beta diversity between nested and idiosyncratic sites; iv) examining whether environmental variables influencing the nestedness of benthic diatom communities are dependent on attachment ability. The results demonstrated a significant nestedness pattern in the benthic diatom metacommunity, and the sampling sites of low attachment species not only exhibited a nestedness pattern, but also with a lower nestedness value compared to the sampling sites of all species. Nested and idiosyncratic species differed in niche width, whereas differences between nested and idiosyncratic species of low attachment species were smaller. Additionally, significant differences in alpha and beta diversity were observed between nested and idiosyncratic sites. Furthermore, it was revealed that the nestedness of benthic diatom metacommunity in our study area were mostly influenced by local environmental variables. Our study contributes to the understanding of the significant nestedness observed in benthic diatom metacommunity in TIL, highlighting its relevance to biodiversity conservation efforts.

Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression.

Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full-length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression-modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra-transcribed region scale. The expMotif-transcribed region combination is the most predominant contributor to the expression-modulating effect of SSRs, and some intra-transcribed regions are critical for this effect. Genes containing the same type of expMotif-SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.

Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae.

Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.