Miracle-dz/UniFAR-FTUs huggingface dataset:
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals

Abstract Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared with their mitochondrial homologs to characterize synonymous to nonsynonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterize 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to noncanonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.
of selection on mitonuclear integrated genes uncover hidden mitogenomic variation

Nuclear copies of mitochondrial genes ( numts ) are commonplace in vertebrate genomes and have been 2 characterized in many species. However, relatively little attention has been paid to understanding their 3 evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes 4 with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of 5 the genes they contain can be compared to their mitochondrial homologs to characterize synonymous 6 to non-synonymous substitution rates, which can shed light on the selection pressures these genes have 7 been subjected to. Here, we characterise 25 numts in the Antarctic fur seal ( Arctocephalus gazella ) 8 genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple 9 substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a 10 historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic 11 region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and 12 their large number of substitutions can be attributed to non-canonical insertions, either the integration 13 of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of 14 pinniped numts and uncovers the presence of hidden sources of mitonuclear variation. 15
Mixing of 30° and 45° Inclined Dense Jets in Shallow Coastal Waters

AbstractThis study experimentally investigates the effect of shallow water depth on the mixing of 30° and 45° inclined dense jets. Three different mixing regimes were identified, namely, the full submergence, plume contact, and centerline impingement regimes. The mixing characteristics in these three regimes, including the jet trajectory and minimum dilution at the water surface (SS) as well as at the return point near the seabed (Sr), were quantified with respect to the densimetric Froude number (F) and cover water depth (H). The nondimensional cover water depth, H/D, was found to be a suitable normalization parameter for shallow water scenarios. The transitional F·D/H among the regimes, the asymptotic limits of the minimum surface dilution at large F, and the various linear coefficients were also determined. Overall, it was found that the surface constraint in the plume contact and centerline impingement regimes, lengthens the jet-spreading distances and reduces the surface dilution, while the bottom di.
Fusarium and allied fusarioid taxa (FUSA). 1

Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species complex (FCCSC) (five species) and the F. concolor species complex (FCOSC) (four species). New species include Fusicolla elongata from soil (Zimbabwe), and Neocosmospora geoasparagicola from soil associated with Asparagus officinalis (Netherlands). New combinations include Neocosmospora akasia, N. awan, N. drepaniformis, N. duplosperma, N. geoasparagicola, N. mekan, N. papillata, N. variasi and N. warna. Newly validated taxa include Longinectria gen. nov., L. lagenoides, L. verticilliforme, Fusicolla gigas and Fusicolla guangxiensis. Furthermore, Fusarium rosicola is reduced to synonymy under N. brevis. Finally, the genome assemblies of Fusarium secorum (CBS 175.32), Microcera coccophila (CBS 310.34), Rectifusarium robinianum (CBS 430.91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952.68) are also announced here. Citation: Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang Q-J, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany J-L, Liu C, Zeng Z-Q, Zhuang W-Y, Yu Z-H, Thines M (2022). Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Systematics and Evolution 9: 161–200. doi: 10.3114/fuse.2022. 09.08
Relating vegetation dynamics to temperature and precipitation at monthly and annual timescales in Taiwan using MODIS vegetation indices

To predict the responses of the timing, duration, and density of photosynthetically active plant cover to a changing climate, it is necessary to first quantitatively describe the relationships between temporal and spatial patterns of vegetation cover and both spatial and inter-annual variation in temperature and precipitation. We examined these relationships at multiple scales in Taiwan using monthly maximum composite values of MODIS-NDVI and MODIS-EVI between 2000 and 2012. The two vegetation indices were highly correlated to each other on a monthly basis for non-forest land-cover types, but correlated poorly in forests, probably due to the saturation of NDVI. However, the two indices were equally sensitive in detecting the onset and offset of growing season for all vegetation types. We found that EVI was positively related to both precipitation and temperature on a monthly timescale, although the relationships were not significant at the annual timescale. The much greater variation in monthly than in annual precipitation and temperature probably explains this difference. At low elevations, precipitation had a positive effect and temperature had a negative effect on EVI; however, at high elevations, which are mostly forested, both were positively related to EVI (although precipitation effects were not significant). We interpret this as evidence of water limitation of photosynthetic cover in the warmer, low-elevation parts of the island, whereas in the higher-elevation areas precipitation was usually adequate to satisfy evapotranspirative demand. This study illustrates the importance of examining the effects of precipitation and temperature on plant growth at a range of spatial and temporal scales. Specifically, finer spatial and temporal scales of analysis may better reveal climatic controls over vegetation growth than broader scales of analysis.
Liquid retention and interfacial area in variably saturated porous media: Upscaling from single‐pore to sample‐scale model

A new model for liquid configuration in angular pore space considering both capillary and adsorptive contributions was proposed as an alternative to the conventional bundle of capillaries representation. In this study we develop a statistical framework for upscaling pore‐scale processes to represent a sample‐scale response of variably saturated porous medium. The representation of pore size distribution by the gamma distribution enables derivation of closed‐form expressions for sample‐scale liquid retention and liquid‐vapor interfacial area. The statistical framework calculates the expected values of liquid configuration as a function of pore geometry and chemical potential considerations. Media properties are used to estimate upscaling parameters by matching model predictions with measured retention data subject to specific surface area constraint. Additionally, a method for estimating liquid‐solid adsorption behavior for the medium is proposed. Model predictions compare favorably with measured retention data, yielding a similar close fit as obtained with the van Genuchten parametric model. Liquid‐vapor interfacial area as a function of chemical potential is readily calculated using the estimated retention parameters. Model calculations of liquid‐vapor interfacial area for sand show reasonable agreement with measurements obtained with surface‐active tracers. The contribution of liquid films dominates the total liquid‐vapor interfacial area and often surpasses the capillary contribution (curved menisci) by several orders of magnitude. This illustrates potential limitations in using cylindrical pore network modeling of interfacial area for multiphase flow predictions. The detailed picture of liquid vapor interfaces provides a sound basis for unsaturated hydraulic conductivity calculations in the sample cross section (i.e., neglecting network effects) and offers insights into microbial habitats and related exchange processes in partially saturated porous media.
Detection of urban warming in recent temperature trends in Japan

The contribution of urban effects on recent temperature trends in Japan was analysed using data at 561 stations for 27 years (March 1979–February 2006). Stations were categorized according to the population density of surrounding few kilometres. There is a warming trend of 0.3–0.4 °C/decade even for stations with low population density (<100 people per square kilometre), indicating that the recent temperature increase is largely contributed by background climatic change. On the other hand, anomalous warming trend is detected for stations with larger population density. Even for only weakly populated sites with population density of 100–300/km2, there is an anomalous trend of 0.03–0.05 °C/decade. This fact suggests that urban warming is detectable not only at large cities but also at slightly urbanized sites in Japan. Copyright © 2008 Royal Meteorological Society
The geographical distribution of the solar semidiurnal surface pressure oscillation

New observations of the solar semidiurnal surface pressure oscillation (S2(P)) at 35 stations throughout the world are presented. These observations are used to supplement those in the literature to produce a large compilation of S2(P) data (403 stations). The geographical distribution of S2(P) is then examined by fitting a series of Hough functions to the station data.
ISOTOPIC (Sr, O, C) INDICATORS OF SALINITY AND TAPHONOMY IN MARGINAL MARINE SYSTEMS

Ten sediment samples from the Crocodile River (Nahal Tanninim), Israel, were analyzed for their foraminiferal abundance and four samples were selected for O, C and Sr isotopic analysis to examine salinity and taphonomic trends. Two biofacies were documented: a Ammonia tepida (59±20% (1σ)) and a Pararotalia spinigera (75±17% (1σ)) dominated assemblage. The distribution of δ 18 O, δ 13 C and 87 Sr/ 86 Sr values within shell material (foraminifera, ostracods, mollusks, algae) documented salinity trends within the open-ended, micro-tidal estuary with greater certainty than paleontological analysis alone. The isotopic data allowed the isolation of taphonomic trends by determining which taxa were transported from their original context. The calculated salinities from the four samples from the Crocodile River had a distribution that was bimodal with the two groups fitting into a marine or very brackish salinity regime. Most of the taxa followed this trend with measured salinities from the 87 Sr/ 86 Sr values in the shell material indicating a relatively stable salinity of 30‰. The mixture of specimens in the death assemblage from such diverse salinity regimes indicated transport both landward and seaward in the estuary. This methodology shows promise as an environmental indicator in brackish systems when replicate sampling and the analysis of live specimens cannot be undertaken.
The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere

The ParB protein forms DNA bridging interactions around parS to condense DNA and earmark the bacterial chromosome for segregation. The molecular mechanism underlying the formation of these ParB networks is unclear. We show here that while the central DNA binding domain is essential for anchoring at parS, this interaction is not required for DNA condensation. Structural analysis of the C-terminal domain reveals a dimer with a lysine-rich surface that binds DNA non-specifically and is essential for DNA condensation in vitro. Mutation of either the dimerisation or the DNA binding interface eliminates ParB-GFP foci formation in vivo. Moreover, the free C-terminal domain can rapidly decondense ParB networks independently of its ability to bind DNA. Our work reveals a dual role for the C-terminal domain of ParB as both a DNA binding and bridging interface, and highlights the dynamic nature of ParB networks in Bacillus subtilis.
New high-pressure granulite event in the Moine Supergroup, northern Scotland: Implications for Taconic (early Caledonian) crustal evolution

Relict high-pressure granulite-facies assemblages have been discovered in mafic sheets within Neoproterozoic Moine Supergroup psammites of northern Scotland. Minerals and fabrics associated with the main 440–430 Ma Caledonian deformation and metamorphism (D2) overprint these assemblages, which preserve peak pressure-temperature ( P-T ) conditions of 11–12 kbar at 650–700 °C, indicating burial to ∼35 km. The maximum age of the sheets is constrained by the post-Grenvillian ca. 1000 Ma age of the youngest detrital zircons in the host psammites. The high- P assemblage is constrained by the age of anatexis in the psammites at 467 ± 10 Ma. Assembling these data with P-T and chronological data for the D2, D3, and later cooling events, two partial clockwise P-T-t-D (time-deformation) paths emerge, demonstrating that the high- P event is not part of the evolution of the P granulite assemblages are interpreted to be a relict of an earlier, Taconic 470–460 Ma history. This new evidence suggests that the tectonic evolution of the Caledonian nappes east of the Moine thrust is more complex than previously thought.
Earth'S Oldest Reported Glaciation: Physical and Chemical Evidence From the Archean Mozaan Group (∼2.9 Ga) of South Africa

The Pongola Supergroup is a thick succession of Archean (∼2.9 Ga) supracrustal rocks in the eastern part of the Kaapvaal craton of southern Africa. Its upper part, the Mozaan Group (∼5000 m‐thick) includes diamictites with a highly varied suite of clasts, some of which are striated and faceted. Clasts in associated stratified siltstones are interpreted as ice‐rafted debris. A glacial origin is also supported by geochemical investigation of diamictite matrix materials and associated mudstones. Plots of SiO2:Al2O3 and TiO2:Al2O3 suggest that these rocks underwent little chemical weathering, an interpretation confirmed by calculation of a Chemical Index of Alteration with low values, typical of other glacial deposits. The analyzed rocks are rich in Fe (average Fe2O3(T) is ∼24% wt %), like rocks of many other glaciomarine successions. The diamictites and associated mudstones of the Mozaan Group have low Th/Sc ratios, suggesting preferential incorporation of mafic materials into the diamictite matrix material. Previous studies suggest that this part of the Kaapvaal craton underwent early cratonization, involving tectonic and plutonic events that may have contributed to the drawdown of atmospheric CO2 and eventually provided a suitable substrate for development of continental glaciers.
Lipophagy: Molecular Mechanisms and Implications in Metabolic Disorders

Autophagy is an intracellular degradation system that breaks down damaged organelles or damaged proteins using intracellular lysosomes. Recent studies have also revealed that various forms of selective autophagy play specific physiological roles under different cellular conditions. Lipid droplets, which are mainly found in adipocytes and hepatocytes, are dynamic organelles that store triglycerides and are critical to health. Lipophagy is a type of selective autophagy that targets lipid droplets and is an essential mechanism for maintaining homeostasis of lipid droplets. However, while processes that regulate lipid droplets such as lipolysis and lipogenesis are relatively well known, the major factors that control lipophagy remain largely unknown. This review introduces the underlying mechanism by which lipophagy is induced and regulated, and the current findings on the major roles of lipophagy in physiological and pathological status. These studies will provide basic insights into the function of lipophagy and may be useful for the development of new therapies for lipophagy dysfunction-related diseases.
Structural and Regulatory Elements of HCV NS5B Polymerase – β-Loop and C-Terminal Tail – Are Required for Activity of Allosteric Thumb Site II Inhibitors

Elucidation of the mechanism of action of the HCV NS5B polymerase thumb site II inhibitors has presented a challenge. Current opinion holds that these allosteric inhibitors stabilize the closed, inactive enzyme conformation, but how this inhibition is accomplished mechanistically is not well understood. Here, using a panel of NS5B proteins with mutations in key regulatory motifs of NS5B – the C-terminal tail and β-loop – in conjunction with a diverse set of NS5B allosteric inhibitors, we show that thumb site II inhibitors possess a distinct mechanism of action. A combination of enzyme activity studies and direct binding assays reveals that these inhibitors require both regulatory elements to maintain the polymerase inhibitory activity. Removal of either element has little impact on the binding affinity of thumb site II inhibitors, but significantly reduces their potency. NS5B in complex with a thumb site II inhibitor displays a characteristic melting profile that suggests stabilization not only of the thumb domain but also the whole polymerase. Successive truncations of the C-terminal tail and/or removal of the β-loop lead to progressive destabilization of the protein. Furthermore, the thermal unfolding transitions characteristic for thumb site II inhibitor – NS5B complex are absent in the inhibitor – bound constructs in which interactions between C-terminal tail and β-loop are abolished, pointing to the pivotal role of both regulatory elements in communication between domains. Taken together, a comprehensive picture of inhibition by compounds binding to thumb site II emerges: inhibitor binding provides stabilization of the entire polymerase in an inactive, closed conformation, propagated via coupled interactions between the C-terminal tail and β-loop.
Velocity variations in carbonate rocks due to dual porosity and wave‐induced fluid flow

Stiffness variations in carbonates may be described as resulting from different concentrations of flat compliant pores or cracks, which can have a significant effect on the effective stiffness and acoustic properties (e.g., velocities and attenuations) of dry as well as saturated carbonates, although they carry extremely little porosity. As shown in this paper, the effects of dual porosity and wave‐induced fluid flow or pore pressure communication may also play a significant role. On the basis of a previously published T‐matrix approach to model the effective viscoelastic properties of cracked porous media, we illustrate the (frequency‐dependent) effects of wave‐induced fluid flow (mainly squirt flow) or pore pressure communication for a model structure consisting of a mixture of fluid‐saturated porous grains and fluid‐saturated cavities (vugs, etc.) that are embedded in a solid matrix associated with carbonates. We assume that the pores within the porous grains are decoupled from the pores in the solid matrix (and possibly saturated with different fluids) but that each pore system at the micro and/or mesoscale may or may not be connected. For each of four different connectivity models, we present numerical results for four different cases of microstructure (that emphasize the importance of cracks and flat compliant pores). Our numerical results indicate that the velocity and attenuation spectra of carbonates vary significantly, even when the crack density and all other volume concentrations are constant.
Spring diurnal cycle of clouds over Tibetan Plateau: Global cloud‐resolving simulations and satellite observations

Thermal forcing of the Tibetan Plateau (TP) has large impacts on the Asian summer monsoon. In this study, we statistically analyzed the outputs from the global cloud‐resolving model, NICAM (Nonhydrostatic ICosahedral Atmospheric Model). In order to investigate the convective activities, two brightness temperature datasets were compared, one derived from the satellite observation and another derived from the model. The model well simulated the spatio‐temporal variations of convective clouds in April 2004. The diurnal cycle of clouds was better represented in NICAM, which shows only few‐hour phase difference, than that in the reanalysis data. Three experiments changing horizontal resolution revealed that the higher resolution run conducts better representation of the diurnal cycle, especially on the nighttime disappearance of the high clouds. These results indicate that the global cloud‐resolving model will improve the seasonal prediction of the Asian summer monsoon through better description on the thermal forcing of the Tibetan Plateau.