Miracle-dz/UniFAR-FTUs huggingface dataset:
Discerning Agricultural Management Effects on Nitrous Oxide Emissions from Conventional and Alternative Cropping Systems: A California Case Study

Several decades of research have provided crucial understanding of the production of nitrous oxide (N2O) from agricultural soils and the major environmental and managerial factors that play a role in the generation of this potent greenhouse gas (GHG). Due to the increase in demand for food production and the concomitant increase in use of N fertilizers to meet this demand, it is more than ever important to quantify the effects of the different factors contributing to N2O emissions and produce detailed, accurate and reliable annual N2O emission budgets for current and alternative agricultural systems. Within the diverse cropping systems of California, annual budgets are missing or incomplete for some of the state’s more important, high acreage cash crops such as grape and nut crops. Recent research, documented within this paper, highlights the difference in N2O emissions between conventional and alternative management practices in perennial and annual cropping systems of California. We observed measureable differences in N2O emissions between standard and conservation irrigation techniques used in a Northern
Summertime canopy albedo is sensitive to forest thinning

Despite an emerging body of literature linking canopy albedo to forest management, understanding of the process is still fragmented. We combined a stand-level forest gap model with a canopy radiation transfer model and satellite-derived model parameters to quantify the effects of forest thinning, that is removing trees at a certain time during the forest rotation, on summertime canopy albedo. The effects of different forest species (pine, beech, oak) and four thinning strategies (light to intense thinning regimes) were examined. During stand establishment, summertime canopy albedo is driven by tree species. In the later stages of stand development, the effect of tree species on summertime canopy albedo decreases in favour of an increasing influence of forest thinning on summertime canopy albedo. These trends continue until the end of the rotation where thinning explains up to 50% of the variance in near-infrared canopy albedo and up to 70% of the variance in visible canopy albedo. More intense thinning lowers the summertime shortwave albedo in the canopy by as much as 0.02 compared to unthinned forest. The structural changes associated with forest thinning can be described by the change in LAI in combination with crown volume. However, forests with identical canopy structure can have different summertime albedo values due to their location: the further north a forest is situated, the more the solar zenith angle increases and thus the higher is the summertime canopy albedo, independent of the wavelength. Despite the increase of absolute summertime canopy albedo values with latitude, the difference in canopy albedo between managed and unmanaged forest decreases with increasing latitude. Forest management thus strongly altered summertime forest albedo.
Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s

During the last few centuries D. melanogaster populations were invaded by several transposable elements, the most recent of which was thought to be the P-element between 1950 and 1980. Here we describe a novel TE, which we named Spoink, that has invaded D. melanogaster. It is a 5216nt LTR retrotransposon of the Ty3/gypsy superfamily. Relying on strains sampled at different times during the last century we show that Spoink invaded worldwide D. melanogaster populations after the P-element between 1983 and 1993. This invasion was likely triggered by a horizontal transfer from the D. willistoni group, much as the P-element. Spoink is probably silenced by the piRNA pathway in natural populations and about 1/3 of the examined strains have an insertion into a canonical piRNA cluster such as 42AB. Given the degree of genetic investigation of D. melanogaster it is surprising that Spoink was able to invade unnoticed.
Walking (and talking) the plank: Dual-task performance costs in a virtual balance-threatening environment

We evaluated the effects of engaging in extemporaneous speech while walking in virtual environments meant to elicit low or high levels of mobility-related anxiety. We expected that mobility-related anxiety imposed by a simulated balance threat (i.e. virtual high elevation) would impair walking behavior and lead to greater dual-task costs. Altogether, 15 adults (age = 25.6 ± 4.7 yrs, 7 women) walked at their self-selected speed within low (ground) and high elevation (15 meters) VR settings while speaking extemporaneously (dual-task) or not speaking (single-task). Likert-scale ratings of cognitive and somatic anxiety, confidence, and mental effort were evaluated after experiencing each condition, and gait speed, step length, and step width, and the variability of each, was calculated for each trial using the position of trackers attached to participants’ ankles. Silent speech pauses (>150ms) were determined from audio recordings to infer the cognitive costs of extemporaneous speech planning at low and high virtual elevation. The presence of a balance threat and the inclusion of a concurrent speech task both perturbed gait kinematics, but only the virtual height illusion increased anxiety and mental effort while decreasing confidence. Extemporaneous speech pauses were longer on average when walking, but no effects of virtual elevation were reported. Trends toward interaction effects arose in self-reported responses, participants reported more comfort walking at virtual heights if they engaged in extemporaneous speech. Walking at virtual elevation and walking while talking have independent and significant effects on gait; both effects were robust and did not support an interaction when combined (i.e., walking and talking at virtual heights). Rather than additive cognitive-motor demands, the nature of extemporaneous speech may have distracted participants from the detrimental effects of walking in anxiety-inducing settings.
Examination of the Quantitative Relationship between Vegetation Canopy Height and LAI

Accurate estimation of vegetation biophysical variables such as the vegetation canopy height () is of great importance to the applications of the land surface models. It is difficult to obtain the data of at the regional scale or larger scale, but the remote sensing provides the most useful and most effective method. The leaf area index (LAI) is closely related to the , and we analyzed its relationship with the correlation analysis based on the dataset at 86 site-years of field measurements from sites worldwide in this study. The result indicates that there is significant positive exponent correlation between these two parameters and the change of LAI would exert great impacts on . The higher the LAI is, the higher the is, and vice versa. Besides, the coefficients of different land cover types are very heterogeneous, and LAI of the needleleaf forest shows strong correlation with , while that of the cropland shows weak correlation with . The results may provide certain reference information for the extraction of the data of at the regional scale with the remote sensing data.
Phosphatidic Acid Dependent Recruitment of Microtubule Motors to Spherical Supported Lipid Bilayers for In-vitro Motility Assays

A variety of membrane-bound vesicles are transported by the kinesin and dynein motor proteins respectively towards plus and minus ends of microtubules inside cells. How specific lipids, particularly rare lipids, bind and activate motors on the vesicle membrane and the biological consequences thereof are poorly understood. Here we prepare spherical supported lipid bilayers (SLBs) consisting of a latex bead enclosed within a membrane that contains phosphatidic acid (PA). When incubated with motor-protein enriched fractions from Dictyostelium or from Rat brain, PA-coated SLBs exhibit robust motion along in-vitro polymerized microtubules. We quantify the activity of SLB-bound motors by measuring their force generation against an Optical trap on polarity-labelled microtubules. Such experiments reveal that PA recruits dynein-dynactin from Dictyostelium, but kinesin-1 from rat brain fractions to drive SLB motion. Kinesin-1 is able to dominate over dynein when dynactin, an activator of dynein, is deficient on SLBs. We demonstrate how inhibiting only kinesin can block both kinesin and dynein activity on a cargo, thus providing an explanation for the long-standing “paradox of co-dependence” in the field of intracellular transport. We also find that as the size of a motor-driven SLB increases, the SLB is able to reverse direction more easily along a microtubule. This observation provides clues as to how micron-sized cargoes are efficiently able to navigate the crowded cytoskeletal space inside cells.
Formation of hemiclonal reproduction and hybridogenesis in Pelophylax water frogs studied with species-specific cytogenomic probes

Meiosis is a conservative process in all sexual organisms which ensures fertility and is central for producing genetic diversity by recombination and random segregation of parental chromosomes. Yet unexplored mechanisms may disrupt it and cause ‘loss of sex’ followed by the emergence of clonal modes of reproduction. Interspecific hybridization is the primary trigger for this process, but mechanistic basis of the transition to asexuality remains still unknown for most vertebrate animals. To study these processes in water frogs, we performed reciprocal mating between two sexual species, Pelophylax ridibundus and P. lessonae, and produced vital F1 progeny (P. esculentus). The RepeatExplorer2 analysis of low-coverage genomic data of the two parental species identified the P. lessonae-specific minisatellite marker PlesSat01-48 (44 bp), which hybridized to (peri)centromeric regions of two chromosome pairs in P. lessonae – the acrocentric chromosome 8 and the chromosome 10 (a carrier of nucleolar organizer region; NOR). Chromosomal mapping combining the novel hybridization probe with the previously designed marker for P. ridibundus-specific centromeric satellite DNA showed that the P. esculentus progeny do not reproduce sexually. Instead, the F1 generation of P. esculentus instantly modified its gametogenesis and established asexual reproduction via hybridogenesis. Gametogenic modifications included premeiotic elimination of one of the parental genomes and clonal propagation of the remaining genome via endoreplication followed by standard meiotic division. The origin of DNA elimination and hybridogenesis in laboratory-produced hybrids supports a hypothesis that P. esculentus arises recurrently in nature whenever parental species come into reproductive contact. Based on the observed pattern of DNA elimination in the F1 progeny we discuss the origin and evolution of population systems in water frogs and the applicability of a newly designed chromosomal probe for other Pelophylax taxa.
Cultivated Robusta coffee meets wild Coffea canephora: Evidence of cultivated-wild hybridisation in the Democratic Republic of the Congo

Background and aims Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure global food security amidst a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridisation with their nearby cultivated crops, posing a significant threat to the wild gene pool. Here, we focussed on Robusta coffee in the Yangambi region in the DR Congo, where cultivated Robusta coffee coexists with its wild relative (Coffea canephora), creating ample opportunity for genetic exchange. We examined the geographical distribution of cultivated Robusta coffee plants and the incidence of hybridisation between cultivated and wild individuals within the rainforest. Methods We used Genotyping-by-Sequencing data from 471 C. canephora individuals across various locations, including natural rainforests, home gardens, and the INERA Coffee Collection, a Robusta coffee field genebank. Our analyses involved establishing robust diagnostic fingerprints that differentiate cultivated from wild coffee, identifying cultivated-wild hybrids and mapping their geographical position. Key results We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where Robusta coffee cultivated in the home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests, which is so far likely not sufficient for the stable incorporation of alleles from the cultivated gene pool into the CWR gene pool. Conclusions The cultivation of Robusta coffee in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high overlap between the cultivated and wild gene pool, together with the relatively low frequency of hybridisation, our results indicate that the overall impact in terms of risk of introgression remains limited so far. Nevertheless, it is important to continue monitoring crop-to-wild gene flow to safeguard the wild gene pool of C. canephora.
Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognised importance in Portugal

Mycobacterium bovis causes animal tuberculosis in livestock and wildlife, with an impact on animal health and production, wildlife management, and public health. In this work, we sampled a multi-host tuberculosis community from the official hotspot risk area of Portugal over 16 years, generating the largest available dataset in the country. Using phylogenetic and ecological modelling, we aimed to reconstruct the history of circulating lineages across the livestock-wildlife interface to inform intervention and the implementation of genomic surveillance within the official eradication plan. We find evidence for the co-circulation of M. bovis European 1 (Eu1), Eu2, and Eu3 clonal complexes, with Eu3 providing sufficient temporal signal for further phylogenetic investigation. The Eu3 most recent common ancestor (bovine) was dated in the 90’s, subsequently transitioning to wildlife (red deer and wild boar). Isolate clustering based on sample metadata was used to inform phylogenetic inference, unravelling frequent transmission between two clusters that represent an ecological corridor of previously unrecognised importance in Portugal. The latter was associated with transmission at the livestock-wildlife interface towards locations with higher temperature and precipitation, lower agriculture and road density, and lower host densities. This is the first analysis of M. bovis Eu3 complex in Iberia, shedding light on background ecological factors underlying long-term transmission, and informing where efforts could be focused within the larger hotspot risk area of Portugal. IMPORTANCE Efforts to strengthen surveillance and control of animal tuberculosis (TB) are ongoing worlwide. Here, we developed an eco-phylodynamic framework based on discrete phylogenetic approaches informed by M. bovis whole genome sequence data representing a multi-host transmission system at the livestock-wildlife interface, within a rich ecological landscape in Portugal, to understand transmission processes and translate this knowledge into disease management benefits. We find evidence for the co-circulation of several M. bovis clades, with frequent transmission of the Eu3 lineage among cattle and wildlife populations. Most transition events between different ecological settings took place toward host, climate and land use gradients, underscoring animal TB expansion and a potential corridor of unrecognised importance for M. bovis maintenance. Results stress that animal TB is an established wildlife disease without ecological barriers, showing that control measures in place are insufficient to prevent long-distance transmission and spillover across multi-host communities, demanding new interventions targeting livestock-wildlife interactions.
Distinct Activation Mechanisms of CXCR4 and ACKR3 Revealed by Single-Molecule Analysis of their Conformational Landscapes

Canonical chemokine receptor CXCR4 and atypical receptor ACKR3 both respond to CXCL12 but induce different intracellular effector responses to regulate cell migration: CXCR4 couples to G proteins and arrestins, while ACKR3 is arrestin-biased. CXCR4 also signals only in response to CXCL12, whereas ACKR3 recruits β-arrestin in response to CXCL12, CXCL12 variants, and other peptides and proteins. To investigate the role of conformational dynamics in the distinct pharmacological behaviors of CXCR4 and ACKR3, we utilized single-molecule FRET. The data revealed that apo CXCR4 preferentially populates a high-FRET inactive state while apo ACKR3 shows little conformational preference, consistent with its promiscuous ligand recognition and propensity for activation. Markedly different conformational landscapes of the receptors in response to ligands suggest that activation of ACKR3 may be achieved by a broader distribution of conformational states than CXCR4. The dynamic properties of ACKR3 may also underly its inability to couple to G proteins, making it arrestin-biased.
Gains in soil C storage under anthropogenic N deposition are rapidly lost following its cessation

Anthropogenic nitrogen (N) deposition enhanced the global terrestrial carbon (C) sink and partially offset anthropogenic CO2 emissions. This was driven by the suppression of microbial activity associated with the breakdown of soil organic matter. However, since the implementation of emission abatement policies in the 1970’s, atmospheric N deposition has declined globally, and the consequences of this decline are unknown. Here, we assessed the response of soil C storage, and associated microbial activities, in a long-term field study that experimentally increased N deposition for 24-years. We measured soil C and N, parameters of microbial activity, and compared effect sizes of soil C in response to, and in recovery from, the N deposition treatment across the history of our experiment (1994-2022). Our results demonstrate that the accumulated C in the organic horizon has been lost and exhibit additional deficits 5-years post-termination of the N deposition treatment. These findings, in part, arise from mechanistic changes in microbial activity. Soil C in the mineral soil was less responsive thus far in recovery. If these organic horizon C dynamics are similar in other temperate forests, the Northern Hemisphere C sink will be reduced and climate warming will be enhanced.
Automated assessments can support regional Red Lists but need to be applied with caution: A case study from central Germany

Aim Expert-based regional Red Lists (RL) carry conservation legislation globally. Yet, they are often difficult to reproduce and their regular compilation by a dwindling number of expert assessors burdens many regional conservation authorities. Here we batch-estimate RL indicators and extinction risk for >1,100 plant species and test the potential of this automated approach to support the expert-based RL process. Location State of Hesse, Central Germany Methods First, we estimated current population status, short-term population trend, long-term population trend, and extinction risk by binning existing occurrence probabilities modelled at three time slices with cut-off values derived from RL methodology. Subsequently we compared the results with the latest version of the Hessian expert-based RL using summary statistics and selected example species. Results We find the assessments of extinction risk to agree in c. 60% of the cases, mostly for species not threatened with extinction. Existing mismatch was by one category in most cases, but up to 6 categories in some cases (mean: 1.6 categories). Furthermore, agreement was highest for extreme categories and very abundant species. Main conclusions Automated assessments were simplistic for many rare and taxonomically challenging species, but we considered them more accurate than the expert assessments for species with intermediate population size and for species of anthropogenic habitats. Furthermore, the automated assessments are particularly informative for the estimation of long-term and short-term population trends, for which experts are often left to guesstimate based on little data.
Adult Human Heart ECM Improves Human iPSC-CM Function via Mitochondrial and Metabolic Maturation

Myocardial infarction can lead to the loss of billions of cardiomyocytes, and while cell-based therapies are a promising option, the immature nature of in vitro-generated human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iCMs) is a significant roadblock to their development. Through the years, various approaches have emerged to improve iCM maturation, yet none could fully recapitulate the complexity of cardiac development and were not enough to achieve full cardiac maturity in vitro. Cardiac differentiation occurs at the early stages of development in a highly dynamic environment. Although significantly improved over the past two decades, small molecule-based iPSC differentiation protocols don’t go beyond producing high purity fetal iCMs. Recently adult extracellular matrix (ECM) was shown to retain tissue memory and has shown some success in driving tissue-specific differentiation in unspecified cells in various organ systems. Therefore, here, we first characterized the adult human heart left ventricle components. We then investigated the effect of adult human heart-derived ECM on iPSC cardiac differentiation and subsequent maturation. By preconditioning iPSCs with ECM, we tested whether creating a cardiac environment around iPSCs would drive them toward cardiac fate before small molecule mediated differentiation. Ultimately, we investigated ECM components that might be responsible for the observed effects. We identified critical glycoproteins and proteoglycans involved in early cardiac development in the adult heart ECM. Namely, adult ECM had extracellular galactin-1, fibronectin, fibrillins, and basement-membrane-specific heparan-sulfate proteoglycan (HSPG), which have been implicated in normal heart development and associated with various embryonic developmental processes. Relatedly, we showed that preconditioning iPSCs with adult ECM resulted in enhanced cardiac differentiation, yielding iCMs with higher functional maturity. Further investigation revealed that a more developed mitochondrial network and coverage as well as enhanced metabolic maturity and a shift towards a more energetic profile allowed the observed functional enhancement in ECM pretreated iCMs. These findings demonstrate the potential of using cardiac ECM for promoting iCM maturation and suggest a promising strategy for improving the development of iCM-based therapies and in vitro cardiac disease modeling and drug screening studies. Upon manipulating ECM, such as heat denaturation and sonication to eliminate protein components and release ECM bound vesicle contents, respectively, we concluded that the beneficial effects that we observed are not solely due to the ECM proteins, and might be related to the decorative units attached to them.