Search Results (35)

Citizen science approaches for monitoring, and even restoring, coral reefs have grown in popularity though tend to be restricted to those who have taken courses that expose them to the relevant methodologies. Now that cheap (~10 USD), waterproof pouches for smart phones are widely available, there is the potential for mass acquisition of coral reef images by non-scientists. Furthermore, with the emergence of better machine-learning-based image classification approaches, high-quality data can be extracted from low-resolution images (provided that key benthic organisms, namely corals, other invertebrates, & algae, can be distinguished). To determine whether informally captured images could yield comparable ecological data to point-intercept + photo-quadrat surveys conducted by highly proficient research divers, we trained an artificial intelligence (AI), CoralNet, with images taken before and during a bleaching event in 2015 in Chagos (Indian Ocean). The overall percent coral covers of the formal, “gold standard” method and the informal, “tourist diver” approach of 38.7 and 35.1%, respectively, were within ~10% of one another; coral bleaching percentages of 30.5 and 31.8%, respectively, were statistically comparable. Although the AI was prone to classifying bleached corals as healthy in ~one-third of cases, the fact that these data could be collected by someone with no knowledge of coral reef ecology might justify this approach in areas where divers or snorkelers have access to waterproof cameras and are keen to document coral reef condition. Full article

The conversion of wetlands into croplands often leads to significant losses of peat soil salinity and soil organic matter (SOM), though quantifying these changes is challenging due to limited historical data. In this study, we compared current soil physicochemical properties with rare historical data from the Mezzano Lowland (ML) in Northeastern Italy, a former wetland drained over 60 years ago. The transformation, which affected approximately 18,100 hectares, was achieved through the construction of a network of drainage canals and pumping stations capable of removing large volumes of water, enabling intensive agricultural use. Results showed a marked decrease in electrical conductivity (EC) and sulphate concentration, indicating extensive salt leaching from the upper peat soil layers. EC dropped from historical values up to 196 $\mathrm{m}$$\mathrm{S}$/cm (1967–1968) to a current maximum of 4.93 $\mathrm{m}$$\mathrm{S}$/cm, while sulphate levels declined by over 90%. SOM also showed significant depletion, especially in deeper layers (50–100 cm), with losses ranging from 50 to 60 $\mathrm{wt}\%$, due to increased aeration and microbial activity post-drainage. These climatic and environmental changes, including a marked reduction in soil salinity and sulphate concentrations due to prolonged leaching, have likely shifted the Mezzano Lowland from a carbon sink to a net source of CO₂ and CH₄ by promoting microbial processes that enhance methane production under anaerobic conditions. To detect residual peat layers, we used Ground-Penetrating Radar (GPR), which, combined with soil sampling, proved effective for tracking long-term peat soil changes. This approach can inform sustainable land management strategies to prevent further carbon loss and maintain peat soil stability. Full article

Species migration or extinction events may occur on a large scale with the intensification of climate change. Plant Species with Extremely Small Populations (PSESP) are more sensitive to climate change as compared to other plants. To date, the potential effect of climate change on Acer yangbiense and Cinnamomum chago, both of which belong to PSESP, remain unknown. In this study, we modeled the distribution dynamics of A. yangbiense and C. chago spanning from the Last Glacial Maximum (LGM) to the end of the 21st century based on the MaxEnt model, optimized using the Kuenm package. The results revealed that the parameter settings of the optimal models were RM (regularization multiplier) = 3.5, FC (feature combination) = QP, and RM = 2, FC = QPT. A. yangbiense and C. chago had AUCs of 0.982 and 0.993, respectively, indicating that the model predictions are highly accurate while effectively balancing complexity and avoiding overfitting. The distribution of A. yangbiense and C. chago was mostly influenced by the precipitation of the driest quarter (bio17) and the min temperature of the coldest month (bio6). From the LGM to the present, the total suitable areas of A. yangbiense and C. chago initially declined before showing a subsequent increase, but it is projected to experience significant reductions in the future, with decreases of 32.98%–64.99% and 63.48%–99.49%, respectively. The distribution centroids of A. yangbiense and C. chago showed a migration trend from south to north from the LGM to the present, and this trend is expected to continue. To enhance the resilience of A. yangbiense and C. chago to meet the challenges of climate change in the future, we proposed that the introduction and artificial cultivation of these species should be carried out in Baoshan, Dali, and Nujiang in the northwest of Yunnan Province, which were the areas with high heat values, so as to expand the populations gradually. Full article

Mesophilic microbial sources of prokaryotic Argonaute (pAgo) programmable nucleases have garnered considerable attention for their potential applications in genome editing and molecular diagnostics. In this study, we characterized a novel pAgo from the mesophilic bacterium Chroococcidiopsis sp. (ChAgo), which can cleave single-stranded DNA (ssDNA) using both 5′-phosphorylated guide DNA (5′P-gDNA) and 5′-hydroxylated guide DNA (5′OH-gDNA). Efficient cleavage occurs using 14–25 nt 5′P-gDNA and 13–20 nt 5′OH-gDNA in the presence of Mn²⁺ ions at temperatures ranging from 25 to 75 °C, with optimal activity at 55 °C. ChAgo demonstrates low tolerance for single-base mismatches, similar to other pAgo proteins. The cleavage efficiency varies based on the guide/target pair, with mismatches at specific positions significantly reducing activity. For instance, mismatches at positions 4, 5, or 12 in T-gDNA/target pairs and at positions 5 or 8–10 in g38NT-gDNA/target pairs notably decrease efficiency. ChAgo’s sensitivity to mismatches makes it a promising tool for nucleic acid manipulation and detection, requiring initial screening for high cleavage efficiency sites and subsequent identification of mismatch positions. Full article

A computational study of X-H···Y binary hydrogen-bonded complexes was undertaken to examine the red- and blue-shifting behavior of three model X-H proton donors interacting with a series of Lewis bases: Y = NH₃, NCLi, NCH, NCF, C₂H₂, BF, CO, N₂ and Ne. Two of these proton donors, FArH and F₃CH, have blue-shifting tendencies, while the third, FH, has red-shifting tendencies. A perturbation theory model for frequency shifts that was derived many years ago was employed to partition the predicted frequency shift into the sum of two components, one dependent on the second derivative of the interaction energy with respect to X-H displacement and the other dependent on the X-H bond length change in the binary complex. The predicted shifts were found to be in good agreement with standard ab initio computations, but they were obtained at much lower computational cost. The change in the infrared intensity of the X-H stretching frequency, expressed as a ratio of complex to monomer intensities, was also investigated, along with its relation to the X-H permanent dipole moment derivative and total induced dipole moment derivative with respect to X-H displacement, and used to rationalize the observed infrared intensity changes in the red- and blue-shifted X-H···Y complexes. Full article

The application of double-stranded RNAs (dsRNAs) to plant surfaces has emerged as a promising tool for manipulating gene expression in plants and pathogens, offering new opportunities for crop improvement. While research has shown the capability of exogenous dsRNAs to silence genes, the full spectrum of their impact, particularly on the intricate network of microRNAs (miRNAs), remains largely unexplored. Here, we show that the exogenous application of chalcone synthase (CHS)-encoding dsRNA to the rosette leaves of Arabidopsis thaliana induced extensive alterations in the miRNA profile, while non-specific bacterial neomycin phosphotransferase II (NPTII) dsRNA had a minimal effect. Two days after treatment, we detected 60 differentially expressed miRNAs among the 428 miRNAs found in the A. thaliana genome. A total of 59 miRNAs were significantly changed after AtCHS-dsRNA treatment compared with water and NPTII-dsRNA, and 1 miRNA was significantly changed after AtCHS-dsRNA and NPTII-dsRNA compared with the water control. A comprehensive functional enrichment analysis revealed 17 major GO categories enriched among the genes potentially targeted by the up- and downregulated miRNAs. These categories included processes such as aromatic compound biosynthesis (a pathway directly related to CHS activity), heterocycle biosynthesis, RNA metabolism and biosynthesis, DNA transcription, and plant development. Several predicted targets of upregulated and downregulated miRNAs, including APETALA2, SCL27, SOD1, GRF1, AGO2, PHB, and PHV, were verified by qRT-PCR. The analysis showed a negative correlation between the expression of miRNAs and the expression of their predicted targets. Thus, exogenous plant gene-specific dsRNAs induce substantial changes in the plant miRNA composition, ultimately affecting the expression of a wide range of genes. These findings have profound implications for our understanding of the effects of exogenously induced RNA interference, which can have broader effects beyond targeted mRNA degradation, affecting the expression of other genes through miRNA regulation. Full article

The genomes and annotated genes of allotetraploid cotton Gossypium hirsutum have been extensively studied in recent years. However, the expression, regulation, and evolution of intergenic genes (ITGs) have not been completely deciphered. In this study, we identified a novel set of actively expressed ITGs in G. hirsutum cotton, through transcriptome profiling based on deep sequencing data, as well as chromatin immunoprecipitation, followed by sequencing (ChIP-seq) of histone modifications and how the ITGs evolved. Totals of 17,567 and 8249 ITGs were identified in G. hirsutum and Gossypium arboreum, respectively. The expression of ITGs in G. hirsutum was significantly higher than that in G. arboreum. Moreover, longer exons were observed in G. hirsutum ITGs. Notably, 42.3% of the ITGs from G. hirsutum were generated by the long terminal repeat (LTR) insertions, while their proportion in genic genes was 19.9%. The H3K27ac and H3K4me3 modification proportions and intensities of ITGs were equivalent to genic genes. The H3K4me1 modifications were lower in ITGs. Additionally, evolution analyses revealed that the ITGs from G. hirsutum were mainly produced around 6.6 and 1.6 million years ago (Mya), later than the pegged time for genic genes, which is 7.0 Mya. The characterization of ITGs helps to elucidate the evolution of cotton genomes and shed more light on their biological functions in the transcriptional regulation of eukaryotic genes, along with the roles of histone modifications in speciation and diversification. Full article

Clonal hematopoiesis (CH), the relative expansion of mutant clones, is derived from hematopoietic stem cells (HSCs) with acquired somatic or cytogenetic alterations that improve cellular fitness. Individuals with CH have a higher risk for hematological and non-hematological diseases, such as cardiovascular disease, and have an overall higher mortality rate. Originally thought to be restricted to a small fraction of elderly people, recent advances in single-cell sequencing and bioinformatics have revealed that CH with multiple expanded mutant clones is universal in the elderly population. Just a few years ago, phylogenetic reconstruction across the human lifespan and novel sensitive sequencing techniques showed that CH can start earlier in life, decades before it was thought possible. These studies also suggest that environmental factors acting through aberrant inflammation might be a common theme promoting clonal expansion and disease progression. However, numerous aspects of this phenomenon remain to be elucidated and the precise mechanisms, context-specific drivers, and pathways of clonal expansion remain to be established. Here, we review our current understanding of the cellular mechanisms driving CH and specifically focus on how pro-inflammatory factors affect normal and mutant HSC fates to promote clonal selection. Full article

Parvovirus infection affects several animal species, especially young animals. In birds, parvovirus infection has been described in Muscovy ducks, turkeys, and chickens, all of which had enteric diseases characterized by diarrhea. Chicken parvovirus (ChPV) has been detected in poultry around the world in animals affected by enteric problems, showing dwarfism, cloacal pasting, and diarrhea. In Brazil, ChPV was detected in chickens affected by diarrhea fifteen years ago. However, the genetic characteristics of ChPV circulating in chicken flocks were not determined. Therefore, the aim of the present investigation was to determine the genetic characteristics of the VP1 gene from ChPV detected in chickens affected by enteric diseases in Brazil. For this purpose, a molecular approach was used. Specific primers were designed to flank the complete VP1 gene of ChPV and amplify it using PCR. The amplified products from samples of chickens with enteric diseases were sequenced, and 22 complete CDs of the VP1 gene were obtained. These samples, compared to the ABU-P1 sequence, showed 17 sequences with high nucleotide (NT) similarity of 92.7–97.4% and amino acid (AA) similarity of 94.8–99.5% associated with Runting and Stunting syndrome (RSS); there were also five samples associated with hens with diarrhea with unusual jejunal dilatation (JD) that had less similarity than the RSS sequences (NT of 86.5% and AA of 93–93.1%). The phylogenetic analysis determined four groups. Group I had sequences from Korea. The second group included sequences from Korea, China, and Brazil (not included in this work). The third group had studied RSS sequences grouped with the ABU-P1 strain and sequences from China and the United States. Finally, the sequences from JD were clustered in a separate group with a bootstrap of 100%, a group that was denoted as group IV, and included sequences from China. RDP4 and SimPlot analysis showed one point of recombination with the sequences of group III ChPV in the JD sequences. Herein, we show that circulating strains of ChPV exhibit genetic differences in the VP1 gene in Brazilian chicken flocks. Nevertheless, more studies are needed to determine the probability of a new genetic group of ChPV based on the analysis of the complete genome. Full article

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids. Full article

We report a broad theoretical study on [(PMe₃)₃MER]⁺ complexes, with M = Ni, Pd, Pt, E = C, Si, Ge, Sn, Pb, and R = Ar^Mes, Tbb, (Ar^Mes = 2,6-dimesitylphenyl; Tbb = C₆H₂-2,6-[CH(SiMe₃)₂]₂-4-^tBu). A few years ago, our group succeeded in obtaining heavier homologues of cationic group 10 carbyne complexes via halide abstraction of the tetrylidene complexes [(PMe₃)₃M=E(X)R] (X = Cl, Br) using a halide scavenger. The electronic structure and the M-E bonds of the [(PMe₃)₃MER]⁺ complexes were analyzed utilizing quantum-chemical tools, such as the Pipek–Mezey orbital localization method, the energy decomposition analysis (EDA), and the extended-transition state method with natural orbitals of chemical valence (ETS-NOCV). The carbyne, silylidyne complexes, and the germylidyne complex [(PMe₃)₃NiGeAr^Mes]⁺ are suggested to be tetrylidyne complexes featuring donor–acceptor metal tetrel triple bonds, which are composed of two strong π(M→E) and one weaker σ(E→M) interaction. In comparison, the complexes with M = Pd, Pt; E = Sn, Pb; and R = Ar^Mes are best described as metallotetrylenes and exhibit considerable M−E−C bending, a strong σ(M→E) bond, weakened M−E π-components, and lone pair density at the tetrel atoms. Furthermore, bond cleavage energy (BCE) and bond dissociation energy (BDE) reveal preferred splitting into [M(PMe₃)₃]⁺ and [ER] fragments for most complex cations in the range of 293.3–618.3 kJ·mol⁻¹ and 230.4–461.6 kJ·mol⁻¹, respectively. Finally, an extensive study of the potential energy hypersurface varying the M−E−C angle indicates the presence of isomers with M−E−C bond angles of around 95°. Interestingly, these isomers are energetically favored for M = Pd, Pt; E = Sn, Pb; and R = Ar^Mes over the less-bent structures by 13–29 kJ·mol⁻¹. Full article

Chitin synthesis has attracted scientific interest for decades as an essential part of fungal biology and for its potential as a target for antifungal therapies. While this interest remains, three decades ago, pioneering molecular studies on chitin synthesis regulation identified the major chitin synthase in yeast, Chs3, as an authentic paradigm in the field of the intracellular trafficking of integral membrane proteins. Over the years, researchers have shown how the intracellular trafficking of Chs3 recapitulates all the steps in the intracellular trafficking of integral membrane proteins, from their synthesis in the endoplasmic reticulum to their degradation in the vacuole. This trafficking includes specific mechanisms for sorting in the trans-Golgi network, regulated endocytosis, and endosomal recycling at different levels. This review summarizes the work carried out on chitin synthesis regulation, mostly focusing on Chs3 as a molecular model to study the mechanisms involved in the control of the intracellular trafficking of proteins. Full article

Methane (CH₄), a powerful greenhouse gas (GHG), has been identified as a key target for emission reduction in the Paris agreement, but it is not currently clear where efforts should be focused to make the greatest impact. Currently, activity data and standard emission factors (EF) are used to generate GHG emission inventories. Many of the EFs are globally uniform and do not account for regional variability in industrial or agricultural practices and/or regulation. Regional EFs can be derived from top–down emissions measurements and used to make bespoke regional GHG emission inventories that account for geopolitical and social variability. However, most large-scale top–down approaches campaigns require significant investment. To address this, lower-cost driving surveys (DS) have been identified as a viable alternative to more established methods. DSs can take top–down measurements of many emission sources in a relatively short period of time, albeit with a higher uncertainty. To investigate the use of a portable measurement system, a 2260 km DS was conducted throughout the Denver–Julesburg Basin (DJB). The DJB covers an area of 8000 km² north of Denver, CO and is densely populated with CH₄ emission sources, including oil and gas (O and G) operations, agricultural operations (AGOs), lakes and reservoirs. During the DS, 157 individual CH₄ emission sources were detected; 51%, 43% and 4% of sources were AGOs, O and G operations, and natural sources, respectively. Methane emissions from each source were quantified using downwind concentration and meteorological data and AGOs and O and G operations represented nearly all the CH₄ emissions in the DJB, accounting for 54% and 37% of the total emission, respectively. Operations with similar emission sources were grouped together and average facility emission estimates were generated. For agricultural sources, emissions from feedlot cattle, dairy cows and sheep were estimated at 5, 31 and 1 g CH₄ head⁻¹ h⁻¹, all of which agreed with published values taken from focused measurement campaigns. Similarly, for O and G average emissions for well pads, compressor stations and gas processing plants (0.5, 14 and 110 kg CH₄ facility⁻¹ h⁻¹) were in reasonable agreement with emission estimates from intensive measurement campaigns. A comparison of our basin wide O and G emissions to measurements taken a decade ago show a decrease of a factor of three, which can feasibly be explained by changes to O and G regulation over the past 10 years, while emissions from AGOs have remained constant over the same time period. Our data suggest that DSs could be a low-cost alternative to traditional measurement campaigns and used to screen many emission sources within a region to derive representative regionally specific and time-sensitive EFs. The key benefit of the DS is that many regions can be screened and emission reduction targets identified where regional EFs are noticeably larger than the regional, national or global averages. Full article

A hemipyridine solvate of bis(pyridine)silver(I) perchlorate, [Agpy₂ClO₄]·0.5py (compound 1) was prepared and characterized by single crystal X-ray analysis and vibrational spectroscopy (R and low-temperature Raman). Compound 1 was prepared via the trituration of [Agpy₂ClO₄] and 4[Agpy₂ClO₄]·[Agpy₄]ClO₄ (as the source of the solvate pyridine) in a mixed solvent of acetone:benzene =1:1 (v = v) at room temperature. The monoclinic crystals of compound 1 were found to be isomorphic with the analogous permanganate complex (a = 19.1093(16) Å, b = 7.7016(8) Å, c = 20.6915(19) Å, β = 105.515(7)°; space group: C2/c). Two [Agpy₂]⁺ cations formed a dimeric unit [Agpy₂ClO₄]₂, and each silver ion was connected to two ClO₄⁻ anions via oxygen atoms. The Ag∙∙∙Ag distance was 3.3873(5) Å, the perchlorate ions were coordinated to silver ions, and the Ag∙∙∙O distances were 2.840(2) Å and 2.8749(16) Å in the centrosymmetric rectangle of Ag-O-Ag-O. The stoichiometric ratio of the monomer [Agpy₂ClO₄] and the solvent pyridine was 1:0.5. The guest pyridine occupied 527.2 ų, which was 18.0% of the volume of the unit cell. There was no additional residual solvent-accessible void in the crystal lattice. The solvate pyridine was connected via its a-CH to one of the O atoms of the perchlorate anion. Correlation analysis, as well as IR and low-temperature Raman studies, were performed to assign all perchlorate and pyridine vibrational modes. The solvate and coordinated pyridine bands in the IR and Raman spectra were not distinguishable. A perchlorate contribution via Ag-O coordination to low-frequency Raman bands was also assigned. Full article

The theory of orientation polarization and dielectric relaxation was developed by P. Debye more than 100 years ago. It is based on approximating a molecule by a sphere having one or more dipole moments. By that the detailed intra- and intermolecular interactions are explicitly not taken into consideration. In this article, the principal limitations of the Debye approximation are discussed. Taking advantage of the molecular specificity of the infrared (IR) spectral range, measurements of the specific IR absorption of the stretching vibration υ(OH) (at 3370 cm⁻¹) and the asymmetric υ_as(CH₂) (at 2862.9 cm⁻¹) are performed in dependence on the frequency and the strength of external electric fields and at varying temperature. The observed effects are interpreted as caused by orientation polarization of the OH and the adjacent CH₂ moieties. Full article