Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective.

Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.

Harvesting electrons and holes from photodriven symmetry-breaking charge separation within a perylenediimide photosynthetic model dimer.

Understanding how to utilize symmetry-breaking charge separation (SB-CS) offers a path toward increasingly efficient light-harvesting technologies. This process plays a central role in the first step of photosynthesis, in which the dimeric "special pair" of the photosynthetic reaction center enters a coherent SB-CS state after photoexcitation. Previous research on SB-CS in both biological and synthetic chromophore dimers has focused on increasing the efficiency of light-driven processes. In a chromophore dimer undergoing SB-CS, the energy of the radical ion pair product is nearly isoenergetic with that of the lowest excited singlet (S1) state of the dimer. This means that very little energy is lost from the absorbed photon. In principle, the relatively high energy electron and hole generated by SB-CS within the chromophore dimer can each be transferred to adjacent charge acceptors to extend the lifetime of the electron-hole pair, which can increase the efficiency of solar energy conversion. To investigate this possibility, we have designed a bis-perylenediimide cyclophane (mPDI2) covalently linked to a secondary electron donor, peri-xanthenoxanthene (PXX) and a secondary electron acceptor, partially fluorinated naphthalenediimide (FNDI). Upon selective photoexcitation of mPDI2, transient absorption spectroscopy shows that mPDI2 undergoes SB-CS, followed by two secondary charge transfer reactions to generate a PXX•+-mPDI2-FNDI•- radical ion pair having a nearly 3 µs lifetime. This strategy has the potential to increase the efficiency of molecular systems for artificial photosynthesis and photovoltaics.

Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis.

Most chemical experiments are planned by human scientists and therefore are subject to a variety of human cognitive biases1, heuristics2 and social influences3. These anthropogenic chemical reaction data are widely used to train machine-learning models4 that are used to predict organic5 and inorganic6,7 syntheses. However, it is known that societal biases are encoded in datasets and are perpetuated in machine-learning models8. Here we identify as-yet-unacknowledged anthropogenic biases in both the reagent choices and reaction conditions of chemical reaction datasets using a combination of data mining and experiments. We find that the amine choices in the reported crystal structures of hydrothermal synthesis of amine-templated metal oxides9 follow a power-law distribution in which 17% of amine reactants occur in 79% of reported compounds, consistent with distributions in social influence models10-12. An analysis of unpublished historical laboratory notebook records shows similarly biased distributions of reaction condition choices. By performing 548 randomly generated experiments, we demonstrate that the popularity of reactants or the choices of reaction conditions are uncorrelated to the success of the reaction. We show that randomly generated experiments better illustrate the range of parameter choices that are compatible with crystal formation. Machine-learning models that we train on a smaller randomized reaction dataset outperform models trained on larger human-selected reaction datasets, demonstrating the importance of identifying and addressing anthropogenic biases in scientific data.

Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics.

Transposable elements (TEs) are selfish genetic elements whose antagonistic interactions with hosts represent a common genetic conflict in eukaryotes. To resolve this conflict, hosts have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, this mechanism is imperfect and fails to fully halt TE replication. Furthermore, TE epigenetic silencing can inadvertently spread repressive marks to adjacent functional sequences, a phenomenon considered a 'curse' of this conflict resolution. Here, we used forward simulations to explore how TE epigenetic silencing and its harmful side effects shape the evolutionary dynamics of TEs and their hosts. Our findings reveal that epigenetic silencing allows TEs and their hosts to stably coexist under a wide range of conditions, because the underlying molecular mechanisms give rise to copy-number dependency of the strength of TE silencing. Interestingly, contrary to intuitive expectations that TE epigenetic silencing should evolve to be as strong as possible, we found a selective benefit for modifier alleles that weaken TE silencing under biologically feasible conditions. These results reveal that the dual nature of TE epigenetic silencing, with both positive and negative effects, complicates its evolutionary trajectory and makes it challenging to determine whether TE epigenetic silencing is a 'blessing' or a 'curse'.

Spin-Frustrated Trisradical Trication of PrismCage.

Organic trisradicals featuring threefold symmetry have attracted significant interest because of their unique magnetic properties associated with spin frustration. Herein, we describe the synthesis and characterization of a triangular prism-shaped organic cage for which we have coined the name PrismCage6+ and its trisradical trication─TR3(•+). PrismCage6+ is composed of three 4,4'-bipyridinium dications and two 1,3,5-phenylene units bridged by six methylene groups. In the solid state, PrismCage6+ adopts a highly twisted conformation with close to C3 symmetry as a result of encapsulating one PF6- anion as a guest. PrismCage6+ undergoes stepwise reduction to its mono-, di-, and trisradical cations in MeCN on account of strong electronic communication between its 4,4'-bipyridinium units. TR3(•+), which is obtained by the reduction of PrismCage6+ employing CoCp2, adopts a triangular prism-shaped conformation with close to C2v symmetry in the solid state. Temperature-dependent continuous-wave and nutation-frequency-selective electron paramagnetic resonance spectra of TR3(•+) in frozen N,N-dimethylformamide indicate its doublet ground state. The doublet-quartet energy gap of TR3(•+) is estimated to be -0.08 kcal mol-1, and the critical temperature of spin-state conversion is found to be ca. 50 K, suggesting that it displays pronounced spin frustration at the molecular level. To the best of our knowledge, this example is the first organic radical cage to exhibit spin frustration. The trisradical trication of PrismCage6+ opens up new possibilities for fundamental investigations and potential applications in the fields of both organic cages and spin chemistry.

Optical Spin Polarization of a Narrow-Linewidth Electron-Spin Qubit in a Chromophore/Stable-Radical System.

Photoexcited organic chromophores appended to stable radicals can serve as qubit and/or qudit candidates for quantum information applications. 1,6,7,12-Tetra-(4-tert-butylphenoxy)-perylene-3,4 : 9,10-bis(dicarboximide) (tpPDI) linked to a partially deuterated α,γ-bisdiphenylene-ß-phenylallyl radical (BDPA-d16 ) was synthesized and characterized by time-resolved optical and electron paramagnetic resonance (EPR) spectroscopies. Photoexcitation of tpPDI-BDPA-d16 results in ultrafast radical-enhanced intersystem crossing to produce a quartet state (Q) followed by formation of a spin-polarized doublet ground state (D0 ). Pulse-EPR experiments confirmed the spin multiplicity of Q and yielded coherence times of Tm =2.1±0.1 µs and 2.8±0.2 µs for Q and D0 , respectively. BDPA-d16 eliminates the dominant 1 H hyperfine couplings, resulting in a single narrow line for both the Q and D0 states, which enhances the spectral resolution needed for good qubit addressability.

Comprehensive Analysis of Glutamate Receptor-like Genes in Rice (Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis.

Glutamate receptors (GLR) are widely present in animals and plants, playing essential roles in regulating plant growth, development and stress response. At present, most studies of GLRs in plants are focused on Arabidopsis thaliana, while there have been few studies on rice. In this study, we identified 26 OsGLR genes in rice (Oryza sativa L.). Then, we analyzed the chromosomal location, physical and chemical properties, subcellular location, transmembrane (TM) helices, signal peptides, three-dimensional (3D) structure, cis-acting elements, evolution, chromatin accessibility, population variation, gene-coding sequence haplotype (gcHap) and gene expression under multiple abiotic stress and hormone treatments. The results showed that out of the 26 OsGLR genes, ten genes had the TM domain, signal peptides and similar 3D structures. Most OsGLRs exhibited high tissue specificity in expression under drought stress. In addition, several OsGLR genes were specifically responsive to certain hormones. The favorable gcHap of many OsGLR genes in modern varieties showed obvious differentiation between Xian/indica and Geng/japonica subspecies. This study, for the first time, comprehensively analyzes the OsGLR genes in rice, and provides an important reference for further research on their molecular function.

Tunable Toxicity of Bufadienolides is Regulated through a Configuration Inversion Catalyzed by a Short-Chain Dehydrogenase/Reductase.

Bufadienolides are toxic components widely found in amphibious toads that exhibit a wide range of biological activities. Guided by UPLC-QTOF-MS analysis, several 3-epi-bufadienolides with unique structures were isolated from the bile of the Asiatic toad, Bufo gargarizans. However, the enzymatic machinery of this epimerization in toads and its significance in chemical ecology remains poorly understood. Herein, we firstly compared the toxicities of two typical bufadienolides, bufalin (featuring a 14ß-hydroxyl) and resibufogenin (containing a 14, 15-epoxy group), with their corresponding 3-epi isomers in a zebrafish model. The results of the toxicology assays showed that the ratio of maximum non-toxic concentrations of these two pairs of compounds are 256 and 96 times, respectively, thereby indicating that 3-hydroxyl epimerization leads to a significant decrease in toxicity. Aiming to investigate the biotransformation of 3-epi bufadienolides in toads, we applied liver lysate to transform bufalin and found that it could stereoselectively catalyze the conversion of bufalin into its 3α-hydroxyl epimer. Following this, we cloned and characterized a short-chain dehydrogenase/reductase, HSE-1, from the toad liver cDNA library and verified its 3(ß→α)-hydroxysteroid epimerization activity. To the best of our knowledge, this is the first hydroxyl epimerase identified from amphibians that regulates the toxicity of animal-derived natural products.

BMDCs induce the generation of the CD103+CD8+ tissue-resident memory T cell subtype, which amplifies local tumor control in the genital tract.

Tissue-resident memory T (Trm) cells can trigger a secondary immune response when they encounter the same antigen, playing an important role in antitumor immunity. However, whether Trm cells are protective against female genital tract tumors remainunknown. Here, we show that cervicovaginal vaccination with HPV16 E7aa43-62peptide/CPG-1826 can generate CD103+CD8+Trm cells in the genital tract. These Trm cells can result in subsequent CD8+ T cell expansion and cytokine production when they encounter the same antigen. Importantly, this secondary response can control rechallenge with tumor cells. In vitro,BMDCs can promote the production of TGF-ß, which induces CD103 expression in CD8+ T cells. In human cervical cancer samples, DCs were correlated with the Trm gene signature, which was positively associated with overall survival. Our results indicate that cervicovaginal Trm cells have the capacity tocontrol tumor growth and that BMDCs may induce Trm cell generation via the TGF-ß signaling pathway.

Expression of immune cell markers and tumor markers in patients with cervical cancer.

OBJECTIVE: Cervical cancer is one of the most common cancers worldwide, and immune function may impact disease progression. Serum markers may also be associated with diagnosis and progression. The aim of this study was to explore the clinical usefulness of determining the levels of peripheral blood immune cells and serum tumor markers in predicting diagnosis and prognosis of patients with cervical cancer. METHODS: 82 patients with cervical cancer (early stage group: IA-IB1 and IIA1; locally advanced group: IB2 and IIA2), 54 patients with cervical intra-epithelial neoplasia (CIN), and 54 healthy women (control group) were recruited. Inclusion criteria were: (1) patients whose cervical lesions were determined based on biopsy; and (2) patients who had not undergone immunotherapy, chemotherapy, or radiotherapy. The exclusion criteria were as follows: (1) patients with a history of other malignant tumors; (2) patients with heart, kidney, and other organ failure; (3) patients with immune diseases; and (4) pregnant or lactating women. The levels of immunocytes and tumor markers were assayed. The relationships among histopathologic factors were analyzed. The correlation between the levels of immunocytes and tumor markers in patients with different degrees of cervical lesions (pre-invasive or cancer) and healthy women was evaluated. RESULTS: The squamous cell carcinoma antigen and carcinoembryonic antigen levels in the control group and the CIN group were significantly lower than those in the cervical cancer groups (p<0.01). The incidence of lymph node metastasis in the early stage and locally advanced groups were 22.9% (11/48) and 46.2% (12/26), respectively, and 58.8% (20/34) and 7.5% (3/37) in the positive and negative lymphovascular invasion groups, respectively (p<0.05). The levels of CD8+ and CD8+ CD28+ T cells in the early stage group were markedly lower than those in the CIN group and the control group (p=0.014, p=0.008, respectively). The ratio of CD4+CD25+/CD4+ in the cervical cancer groups was significantly higher than in the control group (p<0.01). The increased serum squamous cell carcinoma and carcinoembryonic antigen levels and CD4+CD25+/CD4+ ratio were risk factors for cervical cancer by logistic regression analysis (p<0.05). CONCLUSIONS: In patients with cervical cancer, immune function was impaired compared with that in healthy women and patients with CIN, while squamous cell carcinoma and carcinoembryonic antigen levels were increased. Combined detection of the levels of peripheral blood immune cells and serum tumor markers may be helpful for early detection, diagnosis, and prognosis evaluation of patients with cervical cancer.

La(OH)3 nano-rods/polyacrylonitrile nanofibers: fabrication, characterization and application for phosphate removal.

In this study, an excellent phosphate adsorbent was prepared for removing phosphate to an extremely low concentration. The La(OH)3 nano-rods stabilizing in polyacrylonitrile (PAN) nanofibers (PLNFs) were prepared by electrospinning and a subsequent in situ precipitation. PAN nanofibers were employed as the matrix of the composite nanofibers, where the well-dispersed La(OH)3 nano-rods were encapsulated as the active species for highly efficient phosphate capture owing to the strong binding between phosphate and lanthanum. On account of the nano-structure, the maximum phosphate adsorption capacity was 151.98 mg P/g (La), much higher than the result of La(OH)3 nano-crystal, produced by precipitation without PAN or any organic surfactants. Moreover, the PLNFs could remove phosphate (2 mg P/L) to an extremely low concentration within 20 min, which could lead to a nutrient deficient condition to protect water quality and ecosystem. The optimization of PLNFs design was implemented through parameter adjustment of electrospinning. Lanthanum salt content, humidity, concentration of solution and applied voltage were chosen to analyze the influences on the composition, diameter and morphology of the nanofibers, giving the result that the most effective adsorbent was the PLNFs with spider-web-like nano-structures.

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes.

Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity. We measured the transcriptome in a cadmium-enriched diet and a salt-enriched diet for experimental populations of Drosophila melanogaster that evolved for ~130 generations in one of four selective regimes: two constant regimes maintained in either cadmium or salt diets and two heterogeneous regimes that varied either temporally or spatially between the two diets. For populations evolving in constant regimes, we find a strong signature of counter-gradient evolution; the evolved expression differences between populations adapted to alternative diets is opposite to the plastic response of the ancestral population that is naïve to both diets. Based on expression patterns in the ancestral populations, we identify a set of genes for which we predict selection in heterogeneous regimes to result in increases in plasticity and we find the expected pattern. In contrast, a set of genes where we predicted reduced plasticity did not follow expectation. Nonetheless, both gene sets showed a pattern consistent with adaptive expression evolution in heterogeneous regimes, highlighting the difference between observing "optimal" plasticity and improvements in environment-specific expression. Looking across all genes, there is evidence in all regimes of differences in biased allele expression across environments ("allelic plasticity") and this is more common among genes with plasticity in total expression.

Genome-wide patterns of genetic variation within and among alternative selective regimes.

Environmental heterogeneity has been hypothesized to influence levels of genetic variation but the effect of heterogeneity depends on (i) the form of heterogeneity, (ii) whether ecologically relevant or neutral loci are being considered, and (iii) the genetic basis of ecological adaptation. We surveyed genome-wide SNP diversity in replicate experimental Drosophila melanogaster populations with equal census sizes that evolved for 42 generations under one of four selection regimes: (i) salt-enriched environment (Salt), (ii) cadmium-enriched environment (Cad), (iii) temporally (Temp) or (iv) spatially (Spatial) variable environments. There was significant differentiation between all pairs of treatments but the greatest differentiation occurred between the two homogenous treatments (Cad and Salt). For sites likely under differential ecological selection (and those closely linked to them), the pattern of within-population diversity π followed the expectation from classic antagonistic selection theory: Spatial > Temp >S alt ≈ Cad. However, neutral diversity unlinked to selected sites followed a different pattern: Spatial>Salt ≈ Cad > Temp. As implicated by the latter result, measures of FST among replicate populations within treatments are consistent with differences in effective population sizes among selective regimes despite equal census sizes. Though there are clear changes in the rank order of treatments when contrasting selected and neutral sites with respect to π, the rank ordering of treatments with respect to FST appears reasonably consistent between site categories. These results demonstrate that alternative selective regimes affect within- and among-population diversity differently for different site types.

Does Genetic Variation Maintained by Environmental Heterogeneity Facilitate Adaptation to Novel Selection?

Environmental heterogeneity helps maintain genetic variation in fitness. Therefore, one might predict that populations living in heterogeneous environments have higher adaptive potential than populations living in homogeneous environments. Such a prediction could be useful in guiding conservation priorities without requiring detailed genetic studies. However, this prediction will be true only if the additional genetic variation maintained by environmental heterogeneity can be used to respond to novel selection. Here we examine the effect of environmental heterogeneity on future adaptability using replicated experimental Drosophila melanogaster populations that had previously evolved for ∼100 generations under one of four selective regimes: constant salt-enriched larvae medium, constant cadmium-enriched larvae medium, and two heterogeneous regimes that vary either temporally or spatially between the two media. Replicates of these experimental populations were subjected to a novel heat stress while being maintained in their original larval diet selection regimes. Adaptation to increased temperature was measured with respect to female productivity and male siring success after ∼20 generations. For female productivity, there was evidence of adaptation overall and heterogeneous populations had a larger adaptive response than homogeneous populations. There was less evidence of adaptation overall for male siring success and no support for faster adaptation in heterogeneous populations.

Removal of thallium by MnOx coated limestone sand filter through regeneration of KMnO4: Combination of physiochemical and biochemical actions.

Treatment of industrial thallium(Tl)-containing wastewater is crucial for mitigating environmental risks and health threats associated with this toxic metal. The incorporation of Mn oxides (MnOx) into the filtration system is a promising solution for efficient Tl(I) removal. However, further research is needed to elucidate the underlying mechanism behind MnOx-enhanced filtration and the rules of its stable operation. In this study, limestone, a cost-effective material, was selected as the filter media. Raw water with Mn(II), Tl(I), and other pollutants was prepared after a thorough investigation of actual industrial wastewater conditions. KMnO4 was added to induce the formation of MnO2 on limestone surfaces, while long-term operation led to enrichment of manganese oxidizing microorganisms (MnOM). Results revealed a dual mechanism. Firstly, most Mn(II) were oxidized by KMnO4 to form MnO2 attaching to limestone sands, and both Tl(I) and residual Mn(II) were adsorbed onto the newly formed MnO2. Subsequently, enzymes secreted by MnOM facilitated oxidation of remaining Mn(II), resulting in the generation of biogenic manganese oxides (BioMnOx) with numerous vacancies during long-term operation. The generated BioMnOx not only adsorbed Mn(II) and Tl(I) but also promoted their oxidation process. This approach offers an effective and sustainable method for removing both Mn(II) and Tl(I) from industrial wastewater, thereby addressing the challenges posed by thallium-contaminated effluents.

Microelectromechanical system for in situ quantitative testing of tension-compression asymmetry in nanostructures.

Tension-compression asymmetry is a topic of current interest in nanostructures, especially in strain engineering. Herein, we report a novel on-chip microelectromechanical system (MEMS) that can realize in situ quantitative mechanical testing of nanostructures under tension-compression functions. The mechanical properties of three kinds of nanostructures fabricated by focused ion beam (FIB) techniques were systematically investigated with the presented on-chip testing system. The results declare that both Pt nanopillars and C nanowires exhibit plastic deformation behavior under tension testing, with average Young's moduli of 70.06 GPa and 58.32 GPa, respectively. However, the mechanical deformation mechanisms of the two nanostructures changed in compression tests. The Pt nanopillar exhibited in-plane buckling behavior, while the C nanowire displayed 3D twisting behavior with a maximum strain of 25.47%, which is far greater than the tensile strain. Moreover, asymmetric behavior was also observed in the C nanospring during five loading-unloading tension-compression deformation tests. This work provides a novel insight into the asymmetric mechanical properties of nanostructures, with potential applications in nanotechnology research.

Efficacy and safety of acupuncture for painful diabetic neuropathy: a systematic review and meta-analysis.

Background: Painful diabetic neuropathy (PDN) is a common chronic neurological complication of diabetes mellitus. Medications are often used to relieve pain, but with significant side effects. Acupuncture is now a component of pragmatic and integrative treatment for PDN. An increasing number of relevant randomized controlled trials have been published in recent years, but a comprehensive meta-analysis has not yet been performed. The aim of this paper is to verify the effectiveness and safety of acupuncture for PDN by meta-analysis and trial sequential analysis (TSA). Methods: All participants in this study should have had a PDN diagnosis and the trial group was treated with acupuncture. Eight databases, including EMbase, PubMed, Web of science, Cochrane Library, China Biology Medicine disc (CBM), China National Knowledge Infrastructure (CNKI), Wanfang and Chongqing VIP (CQVIP) were retrieved from inception to 5 April 2023. Meta-analysis was conducted utilizing RevMan 5.3 and Stata 15.0. TSA was performed to assess the adequacy of sample size for the outcomes. Results: A total of 36 studies, comprising 2,739 PDN patients, were included. Among them, 1,393 patients were assigned to the trial group and 1,346 patients were treated in the control group. Outcomes covers the primary indicator Total effective rate (RR = 1.42, 95%CI [1.34, 1.52], p < 0.00001), with 21 studies reported, Pain intensity (SMD = -1.27, 95%CI [-1.58, -0.95], p < 0.00001), with 23 studies reported, and other outcomes, including motor nerve conduction velocity (MCV; MD = 3.58, 95%CI [2.77, 4.38], p < 0.00001), sensory nerve conduction velocity (SCV; MD = 3.62, 95%CI [2.75, 4.49], p < 0.00001), Depression score (SMD = -1.02, 95%CI [1.58, 0.46]), Toronto clinical scoring system (TCSS; MD = -2.41, 95%CI [-3.37, -1.45], p < 0.00001), Quality of life (SMD = 1.06, 95%CI [0.66, 1.46]), traditional Chinese medicine (TCM) syndrome score (MD = -4.99, 95%CI [-6.79, -3.18], p < 0.00001), suggesting that acupuncture have an ameliorating effect on PDN in various respect. Egger's test revealed publication bias for four outcomes. TSA showed that as for Total effective rate, Pain Intensity, MCV and SCV, the number of included studies was sufficient to support the conclusions. Conclusion: Acupuncture demonstrates significant effectiveness in improving PDN outcomes, including Total effective rate, Pain intensity, MCV, SCV, Depression score, TCSS, Quality of life, TCM syndrome score. But the Adverse events rate is no different in trail group and control group. The publication bias presented in Total effective rate, Pain intensity, MCV and SCV can be remedied by Trim and filling method. Systematic review registration: Prospero, https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=477295.

Prevalent fast evolution of genes involved in heterochromatin functions.

Heterochromatin is a gene-poor and repeat-rich genomic compartment ubiquitously found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements (TEs). Given the importance of these functions, it is expected that the genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes have been found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compiled an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigated their evolution over both short and long evolutionary time scales in Drosophila. Our analyses found that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number variation, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and irregular disordered regions (IDRs), purifying selection may have maintained the proportions of IDRs. Together with the observed negative associations between rates of protein evolution of these genes and genomic TE abundance, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique molecular features of the heterochromatin environment, while the rapid evolution of TEs may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.

Cotransport of aged biochar colloids and thallium(I) in water-saturated porous media: Impact of the ionic strength, pH and aging degree.

Biochar colloids entering the soil undergo aging over time and exhibit strong capabilities in adsorbing and transporting pollutants. Therefore, investigating the cotransport of aged biochar colloids and thallium (Tl(I)) in quartz sand media is crucial for understanding Tl(I) migration in underground environments. This study investigated the migration of biochar colloids with two different aging degrees and Tl(I) in quartz sand media at various pH and ionic strengths (ISs). The results revealed that under all ISs and pH, 30%AWB (biochar aged with 30 % (w/w) HNO3) inhibited Tl(I) migration in media. This inhibition primarily arose from the introduction of hydroxyl and carboxyl groups during aging, which significantly enhanced colloid adsorption onto Tl(I). At lower ISs, 30%AWB colloids exhibited greater inhibition of Tl(I) migration due to their increased adsorption capacity. Additionally, aging promoted the migration of biochar colloids in the media. Greater biochar aging notably enhanced this promotion, potentially owing to reduced colloidal particle size and the formation of biochar derivatives. Moreover, 50%AWB (biochar aged with 50 % (w/w) HNO3) inhibited Tl(I) migration under low ISs but had almost no impact under high ISs. Nonetheless, at high pH, 50%AWB colloids facilitated Tl(I) migration. This phenomenon might be attributed to the inhibitory effect of aged biochar colloids on Tl(I) adsorption onto media at a high pH, as well as the stable binding between Tl(I) and aged biochar colloids. This study discusses the cotransport of biochar with various degrees of aging and Tl(I) in media, providing insights into remediating soils contaminated with Tl.

Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster.

The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using two new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl (Broman et al. 2003) using additive genetic models. We found 14 quantitative trait loci (QTL) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least one significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.