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1.
Ecol Evol ; 14(7): e11548, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38983701

RESUMO

Plants emit biogenic volatile organic compounds (BVOCs) as signaling molecules, playing a crucial role in inducing resistance against herbivores. Neighboring plants that eavesdrop on BVOC signals can also increase defenses against herbivores or alter growth patterns to respond to potential risks of herbivore damage. Despite the significance of BVOC emissions, the evolutionary rationales behind their release and the factors contributing to the diversity in such emissions remain poorly understood. To unravel the conditions for the evolution of BVOC emission, we developed a spatially explicit model that formalizes the evolutionary dynamics of BVOC emission and non-emission strategies. Our model considered two effects of BVOC signaling that impact the fitness of plants: intra-individual communication, which mitigates herbivore damage through the plant's own BVOC signaling incurring emission costs, and inter-individual communication, which alters the influence of herbivory based on BVOC signals from other individuals without incurring emission costs. Employing two mathematical models-the lattice model and the random distribution model-we investigated how intra-individual communication, inter-individual communication, and spatial structure influenced the evolution of BVOC emission strategies. Our analysis revealed that the increase in intra-individual communication promotes the evolution of the BVOC emission strategy. In contrast, the increase in inter-individual communication effect favors cheaters who benefit from the BVOCs released from neighboring plants without bearing the costs associated with BVOC emission. Our analysis also demonstrated that the narrower the spatial scale of BVOC signaling, the higher the likelihood of BVOC evolution. This research sheds light on the intricate dynamics governing the evolution of BVOC emissions and their implications for plant-plant communication.

2.
Biochemistry (Mosc) ; 89(6): 1079-1093, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38981702

RESUMO

The work presents results of the in vitro and in silico study of formation of amyloid-like structures under harsh denaturing conditions by non-specific OmpF porin of Yersinia pseudotuberculosis (YpOmpF), a membrane protein with ß-barrel conformation. It has been shown that in order to obtain amyloid-like porin aggregates, preliminary destabilization of its structure in a buffer solution with acidic pH at elevated temperature followed by long-term incubation at room temperature is necessary. After heating at 95°C in a solution with pH 4.5, significant conformational rearrangements are observed in the porin molecule at the level of tertiary and secondary structure of the protein, which are accompanied by the increase in the content of total ß-structure and sharp decrease in the value of characteristic viscosity of the protein solution. Subsequent long-term exposure of the resulting unstable intermediate YpOmpF at room temperature leads to formation of porin aggregates of various shapes and sizes that bind thioflavin T, a specific fluorescent dye for the detection of amyloid-like protein structures. Compared to the initial protein, early intermediates of the amyloidogenic porin pathway, oligomers, have been shown to have increased toxicity to the Neuro-2aCCL-131™ mouse neuroblastoma cells. The results of computer modeling and analysis of the changes in intrinsic fluorescence during protein aggregation suggest that during formation of amyloid-like aggregates, changes in the structure of YpOmpF affect not only the areas with an internally disordered structure corresponding to the external loops of the porin, but also main framework of the molecule, which has a rigid spatial structure inherent to ß-barrel.


Assuntos
Porinas , Yersinia pseudotuberculosis , Porinas/química , Porinas/metabolismo , Yersinia pseudotuberculosis/metabolismo , Yersinia pseudotuberculosis/química , Animais , Camundongos , Amiloide/metabolismo , Amiloide/química , Estrutura Secundária de Proteína , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Conformação Proteica
3.
J Environ Manage ; 365: 121579, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38936018

RESUMO

Digital technology advancement provides a significant impetus to achieve China's "dual-carbon" goals, yet it also gives rise to a series of challenges. Therefore, studying the relationship between digital technology innovation and carbon emission efficiency is of paramount importance. This study theoretically analyzes and empirically tests the influence of digital technology innovation (DTI) on total factor carbon emission efficiency (TFCE) using panel data from 268 Chinese cities between 2006 and 2021. The results indicate that: (1) DTI exhibits a "U-shaped" pattern on urban TFCE, with a decrease followed by an increase. (2) Conventional technological innovation (TI) also displays a "U-shaped" relationship with TFCE, with the turning point occurring earlier than that of DTI. DTI surpasses TI in bringing about later-stage improvements in carbon emission efficiency. (3) Mechanism tests reveal that digital technology innovation indirectly affects TFCE through energy effects, technological effects, structural effects, and regulatory effects. (4) The impact of DTI on urban TFCE varies significantly due to differences in geographical location and resource endowments. (5) The development of urban polycentricity advances the turning point at which DTI enhances TFCE while amplifying both the initial "pro-carbon" effect and the subsequent "carbon reduction" effect of DTI. (6) DTI has a spatial spillover effect on urban TFCE. This study provides empirical evidence and policy recommendations for policymakers to advance the digitalization, greening, and decarbonization transformation of cities.

4.
Evol Appl ; 17(5): e13695, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38721593

RESUMO

Recent developments within the IUCN and the Convention on Biological Diversity have affirmed the increasingly key role that effective population size (N e) and the effective size: census size ratio (N e/N) play in applied conservation and management of global biodiversity. This paper reviews and synthesizes information regarding the definition of N e and demographic and genetic methods for estimating effective size, census size, and their ratio. Emphasis is on single-generation estimates of contemporary N e/N, which are the most informative for practical applications. It is crucial to clearly define which individuals are included in the census size (N). Defining N as the number of adults alive at a given time facilitates comparisons across species. For a wide range of applications and experimental designs, inbreeding N e is simpler to calculate and interpret than variance N e. Effects of skewed sex ratio are generally modest, so most reductions to N e/N arise from overdispersed (greater-than-Poisson) variance in offspring number (σk2). Even when fecundity changes with age, overdispersed within-age variance generally contributes most to overall σk2, and both random and deterministic (mediated by selection) factors can be important. Most species are age-structured, so it is important to distinguish between effective size per generation (N e) and the effective number of breeders in one season or year (N b). Both N e and N b are important for applied conservation and management. For iteroparous species, a key metric is variance in lifetime reproductive success (σk•2), which can be affected by a variety of additional factors, including variation in longevity, skip or intermittent breeding, and persistent individual differences in reproductive success. Additional factors that can be important for some species are also discussed, including mating systems, population structure, sex reversal, reproductive compensation, captive propagation, and delayed maturity.

5.
Biol Open ; 13(6)2024 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-38738657

RESUMO

Trait polymorphisms are widespread in nature, and explaining their stable co-existence is a central problem in ecology and evolution. Alternative reproductive tactics, in which individuals of one or more sex exhibit discrete, discontinuous traits in response to reproductive competition, represent a special case of trait polymorphism in which the traits are often complex, behavioural, and dynamic. Thus, studying how alternative reproductive tactics are maintained may provide general insights into how complex trait polymorphisms are maintained in populations. We construct a spatially explicit individual-based model inspired from extensively collected empirical data to address the mechanisms behind the co-existence of three behavioural alternative reproductive tactics in males of a tree cricket (Oecanthus henryi). Our results show that the co-existence of these tactics over ecological time scales is facilitated by the spatial structure of the landscape they inhabit, which serves to equalise the otherwise unequal mating benefits of the three tactics. We also show that this co-existence is unlikely if spatial aspects of the system are not considered. Our findings highlight the importance of spatial dynamics in understanding ecological and evolutionary processes and underscore the power of integrative approaches that combine models with empirical data.


Assuntos
Gryllidae , Reprodução , Comportamento Sexual Animal , Masculino , Gryllidae/fisiologia , Gryllidae/genética , Animais , Evolução Biológica , Fenótipo
6.
Sci Total Environ ; 931: 173010, 2024 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-38710396

RESUMO

In recent years, China has been implementing policies to improve the livestock industry in response to the global trend toward green and low-carbon development. These policies include the establishment of demonstration zones for high-standard agriculture, the relocation of farms to the north, etc. This study aims to investigate the impact of changes in the spatial structure of the livestock industry on methane emissions. It used panel data from 31 provinces in China from 2001 to 2021 and applied the IPCC methodology to quantify methane emissions at both the national and provincial levels. In addition, a spatial econometric model was used to analyze the impact of changes in the spatial structure of the livestock industry on methane emissions. The results show that methane from livestock in China decreased from 13.85 million tons in 2001 to 11.82 million tons in 2021. In addition, methane emissions from livestock in China show a significant spatial gradient and correlation. The Southwest has the highest methane emissions, accounting for 24 % of the total emissions. After controlling for spatial correlation and other factors in the model, it was found that the spatial structure of the livestock industry has a different influence on methane emissions both in the province and in neighboring provinces. To improve methane emission efficiency in the future, policies such as establishing functional zones for livestock farming, strengthening technological innovation and sharing for green development in agriculture, and promoting the optimization of agricultural and rural management structures should be implemented.

7.
ISME J ; 18(1)2024 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-38691424

RESUMO

Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.


Assuntos
Antibacterianos , Escherichia coli , Salmonella enterica , Simbiose , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Antibacterianos/farmacologia , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/genética , Técnicas de Cocultura , Interações Microbianas , Ampicilina/farmacologia , Farmacorresistência Bacteriana
8.
Am Nat ; 203(6): 668-680, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38781525

RESUMO

AbstractMaintaining the stability of ecological communities is critical for conservation, yet we lack a clear understanding of what attributes of metacommunity structure control stability. Some theories suggest that greater dispersal promotes metacommunity stability by stabilizing local populations, while others suggest that dispersal synchronizes fluctuations across patches and leads to global instability. These effects of dispersal on stability may be mediated by metacommunity structure: the number of patches, the pattern of connections across patches, and levels of spatiotemporal correlation in the environment. Thus, we need theory to investigate metacommunity dynamics under different spatial structures and ecological scenarios. Here, we use simulations to investigate whether stability is primarily affected by connectivity, including dispersal rate and topology of connectivity network, or by mechanisms related to the number of patches. We find that in competitive metacommunities with environmental stochasticity, network topology has little effect on stability on the metacommunity scale even while it could change spatial diversity patterns. In contrast, the number of connected patches is the dominant factor promoting stability through averaging stochastic fluctuations across more patches, rather than due to more habitat heterogeneity per se. These results broaden our understanding of how metacommunity structure changes metacommunity stability, which is relevant for designing effective conservation strategies.


Assuntos
Ecossistema , Modelos Biológicos , Dinâmica Populacional , Biota , Distribuição Animal , Processos Estocásticos , Meio Ambiente , Simulação por Computador
9.
Proc Biol Sci ; 291(2023): 20232559, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38808450

RESUMO

The spatial structure of populations is key to many (eco-)evolutionary processes. In such cases, the strength and sign of selection on a trait may depend on the spatial scale considered. An example is the evolution of altruism: selection in local environments often favours cheaters over altruists, but this can be outweighed by selection at larger scales, favouring clusters of altruists over clusters of cheaters. For populations subdivided into distinct groups, this effect is described formally by multilevel selection theory. However, many populations do not consist of non-overlapping groups but rather (self-)organize into other ecological patterns. We therefore present a mathematical framework for multiscale selection. This framework decomposes natural selection into two parts: local selection, acting within environments of a certain size, and interlocal selection, acting among them. Varying the size of the local environments subsequently allows one to measure the contribution to selection of each spatial scale. To illustrate the use of this framework, we apply it to models of the evolution of altruism and pathogen transmissibility. The analysis identifies how and to what extent ecological processes at different spatial scales contribute to selection and compete, thus providing a rigorous underpinning to eco-evolutionary intuitions.


Assuntos
Altruísmo , Evolução Biológica , Seleção Genética , Animais , Modelos Biológicos , Dinâmica Populacional
10.
Genetics ; 227(2)2024 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-38639307

RESUMO

Spatially resolved datasets are revolutionizing knowledge in molecular biology, yet are under-utilized for questions in evolutionary biology. To gain insight from these large-scale datasets of spatial organization, we need mathematical representations and modeling techniques that can both capture their complexity, but also allow for mathematical tractability. Evolutionary graph theory utilizes the mathematical representation of networks as a proxy for heterogeneous population structure and has started to reshape our understanding of how spatial structure can direct evolutionary dynamics. However, previous results are derived for the case of a single new mutation appearing in the population and the role of network structure in shaping fitness landscape crossing is still poorly understood. Here we study how network-structured populations cross fitness landscapes and show that even a simple extension to a two-mutational landscape can exhibit complex evolutionary dynamics that cannot be predicted using previous single-mutation results. We show how our results can be intuitively understood through the lens of how the two main evolutionary properties of a network, the amplification and acceleration factors, change the expected fate of the intermediate mutant in the population and further discuss how to link these models to spatially resolved datasets of cellular organization.


Assuntos
Evolução Molecular , Aptidão Genética , Modelos Genéticos , Mutação , Genética Populacional
11.
Cell Rep ; 43(4): 114106, 2024 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-38625795

RESUMO

Heterogeneity in gene expression is common among clonal cells in bacteria, although the sources and functions of variation often remain unknown. Here, we track cellular heterogeneity in the bacterium Pseudomonas aeruginosa during colony growth by focusing on siderophore gene expression (pyoverdine versus pyochelin) important for iron nutrition. We find that the spatial position of cells within colonies and non-genetic yet heritable differences between cell lineages are significant sources of cellular heterogeneity, while cell pole age and lifespan have no effect. Regarding functions, our results indicate that cells adjust their siderophore investment strategies along a gradient from the colony center to its edge. Moreover, cell lineages with below-average siderophore investment benefit from lineages with above-average siderophore investment, presumably due to siderophore sharing. Our study highlights that single-cell experiments with dual gene expression reporters can identify sources of gene expression variation of interlinked traits and offer explanations for adaptive benefits in bacteria.


Assuntos
Regulação Bacteriana da Expressão Gênica , Fenóis , Pseudomonas aeruginosa , Sideróforos , Sideróforos/metabolismo , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Oligopeptídeos/metabolismo , Oligopeptídeos/genética , Ferro/metabolismo , Tiazóis/metabolismo
12.
Ying Yong Sheng Tai Xue Bao ; 35(2): 298-306, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38523086

RESUMO

Based on the continuous inventory data of forest resources in Zhejiang Province in 2019 and 2021, we used statistical methods such as polynomial regression to analyze the impacts of topography and forest spatial structure on average annual diameter at breast height (DBH) growth of main pioneer tree species in natural broad-leaved mixed forests. The results showed that DBH of Schima superba, Quercus glauca, Quercus fabri, Lithocarpus glaber, Castanopsis eyrei, and Castanopsis sclerophylla were between 5-50.8, 5-41.5, 5-50.8, 5-43.9, 5-55.5, and 5-46.1 cm, respectively. We classified all the trees into three classes based on DBH: small (6-12 cm), medium (12-14 cm), and large (>26 cm). The average annual DBH growth of S. superba and Q. glauca was the highest on semi-shady slope and shady slope, with increases of 2.9%-15.7% and 1.1%-41.2%, respectively. The average annual DBH growth of large-diameter S. superba, L. glaber, C. eyrei and C. sclerophylla decreased with the increase of slope, with a maximum decrease of 27.0% for S. superba, with no significant difference among small- and medium-diameter trees as a whole. The slope position did not affect the annual DBH growth of small-diameter trees, while that of medium- and large-diameter S. superba, Q. glauca, and large-diameter Q. fabri, L. glaber decreased with the change of slope position from downhill, mesoslope, uphill to ridge, with a maximum decrease of 28.1% for L. glabe, and the major-diameter C. eyrei was on the contrary. Appropriate increase in the mingling was beneficial to the average annual DBH growth of medium- and large-diameter trees. Moderate mixing was suitable for S. superba, while low degree mixing and moderate mixing was suitable for Q. glauca, Q. fabri and L. glaber, and intensive mixing was suitable for C. eyrei and C. sclerophylla. No significant difference was observed for minor-diameter trees under the mingling. The neighborhood comparison only had a significant effect on the average annual DBH growth of large-diameter Q. glauca, Q. fabri, and L. glaber, which was significantly higher under subdominance-moderation than moderation-inferiority. The average annual DBH growth in the study area was mainly affected by aspect and mixing degree.


Assuntos
Pinus , Quercus , Árvores , Florestas , China
13.
Adv Mater ; 36(23): e2313388, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38350631

RESUMO

Organic electrode materials (OEMs) have gathered extensive attention for aqueous zinc-ion batteries (AZIBs) due to their structural diversity and molecular designability. However, the reported research mainly focuses on the design of the planar configuration of OEMs and does not take into account the important influence of the spatial structure on the electrochemical properties, which seriously hamper the further performance liberation of OEMs. Herein, this work has designed a series of thioether-linked naphthoquinone-derived isomers with tunable spatial structures and applied them as the cathodes in AZIBs. The incomplete conjugated structure of the elaborately engineered isomers can guarantee the independence of the redox reaction of active groups, which contributes to the full utilization of active sites and high redox reversibility. In addition, the position isomerization of naphthoquinones on the benzene rings changes the zincophilic activity and redox kinetics of the isomers, signifying the importance of spatial structure on the electrochemical performance. As a result, the 2,2'-(1,4-phenylenedithio) bis(1,4-naphthoquinone) (p-PNQ) with the smallest steric hindrance and the most independent redox of active sites exhibits a high specific capacity (279 mAh g-1), an outstanding rate capability (167 mAh g-1 at 100 A g-1), and a long-term cycling lifetime (over 2800 h at 0.05 A g-1).

14.
Environ Sci Ecotechnol ; 20: 100375, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38283869

RESUMO

Bioelectrochemical systems (BES) have emerged as a dual-function technology for treating wastewater and recovering energy. A vital element of BES is the rapid formation and maintenance of electroactive biofilms (EABs). Previous attempts to accelerate EAB formation and improve electroactivities focused on enhancing the bacterial adhesion process while neglecting the rate-limiting step of the bacterial transport process. Here, we introduce membrane filtration into BES, establishing a dynamic membrane filtration system that enhances overall performance. We observed that optimal membrane flux considerably reduced the startup time for EAB formation. Specifically, EABs established under a 25 L m-2 h-1 flux (EAB25 LMH) had a formation time of 43.8 ± 1.3 h, notably faster than the 51.4 ± 1.6 h in the static state (EAB0 LMH). Additionally, EAB25 LMH exhibited a significant increase in maximum current density, approximately 2.2 times higher than EAB0 LMH. Pearson correlation analysis indicated a positive relationship between current densities and biomass quantities and an inverse correlation with startup time. Microbial analysis revealed two critical findings: (i) variations in maximum current densities across different filtration conditions were associated with redox-active substances and biomass accumulation, and (ii) the incorporation of a filtration process in EAB formation enhanced the proportion of viable cells and encouraged a more diverse range of electroactive bacteria. Moreover, the novel electroactive membrane demonstrated sustained current production and effective solid-liquid separation during prolonged operation, indicating its potential as a viable alternative in membrane-based systems. This approach not only provides a new operational model for BES but also holds promise for expanding its application in future wastewater treatment solutions.

15.
Sci Total Environ ; 912: 169131, 2024 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-38070575

RESUMO

In this paper, the effects of species diversity, tree growth, and spatial clustering on mycorrhizal carbon and nitrogen sequestration and the interaction of soil physicochemical properties in Northeast China were investigated. Based on 720 10 m ∗ 10 m plots in Harbin Experimental Forest Farm of Northeast Forestry University, we determined mycorrhizal biomarkers of easily extractable Glomalin-related soil protein (EEG) and total Glomalin-related soil protein (TG). Four plant diversity indices, seven structural metrics, and five soil properties were also measured. We found that: 1) The low tree diversity plots had 1.08-1.23 times higher TG, EEG, TG-N/TN (proportion of N in TG to TN), and TG-C/SOC (proportion of C in TG to SOC) than the high plots. 2) Tree diameter was negatively correlated with EEG and TG, but positively correlated with the EEG and TG contribution to soil TN and SOC. Soil EEG and TG were positively correlated with under-branch height and tree density. W (Uniform Angle Index, higher W indicates more clustering of tree distribution in the plot) was negatively correlated with the above four ratios and positively correlated with EEG/TG. 3) pH was the most powerful explainer for the GRSP variations (6.8 %, strongest negative association with GRSP/TN, R2 > 0.13), followed by soil electrical conductance (6.5 %, positive relation with TG, p < 0.05), AP (3.2 %). 4) Plant diversity mainly affected GRSP traits through the interaction with soils (0.07), tree growth and density directly increased TG, TG-N/TN, and TG-C/SOC, while tree spatial distribution directly reduced TG-N/TN. Our finding highlighted the important effects of tree diversity and forest structural traits on GRSP amount, carbon sequestration, and nutrient retentions, and could support glomalin-related forest soil management of temperate forests in the high-latitude northern hemisphere.


Assuntos
Micorrizas , Solo , Humanos , Solo/química , Árvores/metabolismo , Micorrizas/metabolismo , Florestas , Proteínas Fúngicas/metabolismo , Glicoproteínas/metabolismo , China , Carbono/análise
16.
Int J Biol Macromol ; 256(Pt 2): 127574, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37952797

RESUMO

Gel property is one of the most important abilities to endow protein-based food products with a unique texture and higher overall acceptability. Cereal ß-glucan (BG) is widely applied in protein-based products to improve the stability of the protein gel by increasing water holding capacity, storage modulus (G'), loss modulus (G") and linking with protein through more exposed sites, making it easier to form a stronger three-dimensional gel network. In addition, BG may be cross-linked with proteins, or physically embedded and covered in protein network structures, interacting with proteins mainly through non-covalent bonds including hydrogen bonding and electrostatic interaction. Furthermore, the transition of the α-helix to the ß-form in the protein secondary structure also contributes to the stability of the protein gel. The practical applications of BG from different cereals in protein-based products are summarized, and the rheological properties, microstructure of protein as well as the underlying interaction mechanisms between BG and protein are discussed. In conclusion, cereal BG is a promising polysaccharide in developing nutritional protein-based products with better sensory properties.


Assuntos
beta-Glucanas , beta-Glucanas/química , Reologia , Polissacarídeos , Géis/química
17.
Plant J ; 117(1): 33-52, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37731059

RESUMO

Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.


Assuntos
Cromatina , Zea mays , Cromatina/genética , Zea mays/genética , Metilação de DNA , Montagem e Desmontagem da Cromatina/genética , Inativação Gênica , Regulação da Expressão Gênica de Plantas
18.
J Fish Biol ; 104(3): 681-697, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37837280

RESUMO

Population monitoring of Atlantic salmon (Salmo salar L.) abundance is an essential element to understand annual stock variability and inform fisheries management processes. Smolts are the life stage marking the transition from the freshwater to the marine phase of anadromous Atlantic salmon. Estimating smolt abundance allows for subsequent inferences on freshwater and marine survival rates. Annual abundances of out-migrating Atlantic salmon smolts were estimated using Bayesian models and an 18-year capture-mark-recapture time series from two to five trapping locations within the Restigouche River (Canada) catchment. Some of the trapping locations were at the outlet of large upstream tributaries, and these sampled a portion of the total out-migrating population of smolts for the watershed, whereas others were located just above the head of tide of the Restigouche River and sampled the entire run of salmon smolts. Due to logistic and environmental conditions, not all trapping locations were operational each year. Additionally, recapture rates were relatively low (<5%), and the absolute number of recaptures was relatively few (most often a few dozen), leading to incoherent and highly uncertain estimates of tributary-specific and whole catchment abundance estimates when the data were modeled independently among trapping locations and years. Several models of increasing complexity were tested using simulated data, and the best-performing model in terms of bias and precision incorporated a hierarchical structure among years on the catchability parameters and included an explicit spatial structure to account for the annual variations in the number of sampled locations within the watershed. When the best model was applied to the Restigouche River catchment dataset, the annual smolt abundance estimates varied from 250,000 to 1 million smolts, and the subbasin estimates of abundance were consistent with the spatial structure of the monitoring programme. Ultimately, increasing the probabilities of capture and the absolute number of recaptures at the different traps will be required to improve the precision and reduce the bias of the estimates of smolt abundance for the entire basin and within subbasins of the watershed. The model and approach provide a significant improvement in the models used to date based on independent estimates of abundance by trapping location and year. Total abundance and relative production in discrete spawning, nesting, or rearing areas provide critical information to appropriately understand and manage the threats to species that can occur at subpopulation spatial scales.


Assuntos
Salmo salar , Animais , Teorema de Bayes , Migração Animal , Canadá , Água Doce , Rios
19.
Urologiia ; (6): 64-67, 2023 Dec.
Artigo em Russo | MEDLINE | ID: mdl-38156685

RESUMO

AIM: To study the efficiency of pre-administration of a peptide mimicking the spatial structure of erythropoietin -chain B in modeling experimental post-contrast acute kidney injury. MATERIALS AND METHODS: In this study, an experimental model of post-contrast acute kidney injury was created using a non-steroidal anti-inflammatory drug, a nitric oxide synthase inhibitor, and injection of iopromide to mature male mice. After 48 hours, a comprehensive assessment of the concentration of creatinine, urea, glomerular filtration rate, the ratio of urea/albumin in the serum, as well as the level of proteinuria and interleukin 6 in the urine was carried out. RESULTS: A peptide mimicking the spatial structure of erythropoietin -chain B, administered at a dose of 100 g/kg 30 minutes before modeling of pathologic process, contributes to a significant decrease in creatinine and urea concentrations by 2.5 and 1.8 times, respectively, with an increase in glomerular filtration rate 4.4 times. In addition, in the group with pharmacological correction, there was a significant decrease in the ratio of urea/albumin by 2.2 times, a decrease in the level of proteinuria by 61.9% and a decrease in the concentration of pro-inflammatory interleukin-6 in the urine by 2.1 times. CONCLUSION: Thus, the preliminary administration of a peptide that mimics the spatial structure of the erythropoietin -chain B helps to reduce the severity of post-contrast acute kidney injury in the experiment, due to anti-inflammatory properties.


Assuntos
Injúria Renal Aguda , Eritropoetina , Masculino , Camundongos , Animais , Creatinina/uso terapêutico , Eritropoetina/farmacologia , Eritropoetina/uso terapêutico , Injúria Renal Aguda/induzido quimicamente , Peptídeos/uso terapêutico , Proteinúria/patologia , Ureia/uso terapêutico , Albuminas/uso terapêutico , Anti-Inflamatórios/uso terapêutico , Rim/patologia
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