Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the accuracy of paired and random sampling for quantifying plant–plant interactions in natural communities

Interactions among plant species in extreme ecological systems are often inferred from spatial associations and quantified by means of paired sampling. Yet, this method might be confounded by habitat-sharing effects, in particular when microenvironmental heterogeneity and stress are high. Here, we address whether paired and random sampling methods provide similar results at varying levels of environmental heterogeneity. Furthermore, we investigate how the relationship between species preferences and abiotic severity influences the outcome of these two methods. We quantified spatial associations with the two methods at three sites that encompass different micro-environmental heterogeneity and stress levels: semi-arid environments in Canary Islands, Spain and Sardinia, Italy and a cold alpine environment in Hokkaido (Japan). Then, we simulated plant communities with different levels of species micro-habitat preferences, environmental heterogeneity and stress levels. We found that differences in species associations between paired and random sampling were indistinguishable from zero in our model simulations. At each site, there were strong differences between beneficiary species in their spatial association with benefactor species, and associations became more positive with increasing stress in Spain. Most importantly, there were no differences in the results yielded by the two methods at any of the different stress levels at the Spanish and Japanese sites. At the Italian site, although micro-environmental heterogeneity was low, we found weakly significant differences between methods that were unlikely due to habitat-sharing effects. We conclude that the paired sampling method can provide significant insights into net, long-term effects of plant interactions in spatially conspicuous environments.
The phosphatase Glc7 controls the eisosomal response to starvation via post-translational modification of Pil1

The yeast plasma membrane (PM) is organised into specific subdomains that regulate surface membrane proteins. Surface transporters actively uptake nutrients in particular regions of the PM where they are also susceptible to substrate induced endocytosis. However, transporters also diffuse into distinct subdomains termed eisosomes, where they are protected from endocytosis. Although most nutrient transporter populations are downregulated in the vacuole following glucose starvation, a small pool is retained in eisosomes to provide efficient recovery from starvation. We find the core eisosome subunit Pil1, a Bin, Amphiphysin and Rvs (BAR) domain protein required for eisosome biogenesis, is phosphorylated primarily by the kinase Pkh2. In response to acute glucose starvation, Pil1 is rapidly dephosphorylated. Enzyme localisation and activity screens implicate the phosphatase Glc7 is the primary enzyme responsible for Pil1 dephosphorylation. Both depletion of GLC7 and phospho-ablative or phospho-mimetic mutations of Pil1 correlate with Pil1 phosphorylation status, failure to properly retain transporters in eisosomes, and results in defective starvation recovery. We propose precise posttranslational control of Pil1 modulates nutrient transporter retention within eisosomes depending on extracellular nutrient levels, to maximise recovery following starvation.
Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes

Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect large-scale cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules upon germinal vesicle breakdown is achieved by the combined activities of yolk granule fusion and microtubule aster formation and translocation. We find that cortical granules are moved towards the oocyte surface through radially-outward cytoplasmic flows induced by yolk granules fusing within the oocyte center in response to GV breakdown. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with cortical granules at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GV breakdown, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of cortical granules by Rab11 at the oocyte surface is needed for cortical granule release and subsequent chorion elevation, a process central in oocyte activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in determining cytoplasmic organization during oocyte maturation.
The transcriptional regulator JAZ8 interacts with the C2 protein from geminiviruses and limits the viral infection in Arabidopsis

Jasmonates (JAs) are phytohormones that finely regulate critical biological processes, including plant development and defense. JASMONATE ZIM-DOMAIN (JAZ) proteins are crucial keeping JA-responsive genes in a repressed state. In the presence of JA-Ile, JAZ repressors are ubiquitinated and targeted for degradation by the ubiquitin/proteasome system, allowing the activation of the downstream transcription factors and, consequently, the activation of JA-responsive genes. A growing body of evidence has shown that JA signalling is crucial in defending against plant viruses and their insect vectors. Here, we describe the interaction of C2 proteins from two geminiviruses from the genus Begomovirus, tomato yellow curl Sardinia virus (TYLCSaV) and tomato yellow leaf curl virus (TYLCV), with the transcriptional repressor JAZ8 from Arabidopsis thaliana and its closest orthologue in tomato, SlJAZ9. Both JAZ and C2 proteins colocalize in the nucleus, forming discrete nuclear speckles. Overexpression of JAZ8 did not lead to altered responses to TYLCV infection; however, knock-down of JAZ8 favours the geminiviral infection in plants. Low levels of JAZ8 likely affect the viral infection specifically since JAZ8-silenced plants do not display developmental phenotypes nor present differences in their interaction with the viral insect vector. Our results show that JAZ8 interacts with geminiviral C2 proteins and exerts an anti-geminiviral effect.
Facilitation–inhibition control of motor neuronal persistent inward currents in young and older adults

A well-coordinated control of motor neuronal persistent inward currents (PICs) via diffuse neuromodulation and local inhibition is essential to ensure motor units discharge at required times and frequencies. Current best estimates indicate that PICs are reduced in older adults; however, it is not yet known whether PIC facilitation-inhibition control is also altered with ageing. We investigated the responses of PICs to i) a remote handgrip contraction, which is believed to diffusely increase serotonergic input onto motor neurones, and ii) tendon vibration of the antagonist muscle, which elicits reciprocal inhibition, in both young and older adults. High-density surface electromyograms were collected from soleus and tibialis anterior of 18 young and 26 older adults during triangular-shaped plantar and dorsiflexion contractions to 20% (handgrip experiments) and 30% (vibration experiments) of maximum torque (rise-decline rate of 2%/s). The paired-motor-unit analysis was used to calculate ΔF, which is assumed proportional to PIC strength. ΔF increased in both soleus (0.55pps, 16.0%) and tibialis anterior (0.42pps, 11.4%) during the handgrip contraction independent of age. However, although antagonist tendon vibration reduced ΔF in soleus (0.28pps, 12.6%) independent of age, less reduction was observed in older (0.42pps, 10.7%) than young adults (0.72pps, 17.8%) in tibialis anterior. Our data indicate a preserved ability of older adults to amplify PICs following a remote handgrip contraction, during which increased serotonergic input onto the motor neurones is expected, in both lower leg muscles. However, PIC deactivation in response to reciprocal inhibition was impaired with ageing in tibialis anterior despite being preserved in soleus. KEYPOINTS Motor neuronal persistent inward currents (PICs) are amplified via diffuse neuromodulation and deactivated by local inhibition to ensure motor units discharge at required times and frequencies, allowing a normal motor behaviour. PIC amplitudes appear to be reduced with ageing, however it is not known whether PIC facilitation-inhibition control is also altered. Remote handgrip contraction, which should diffusely increase serotonergic input onto motor neurones, amplified PICs similarly in both soleus and tibialis anterior of young and older adults. Antagonist tendon vibration, which induces reciprocal inhibition, reduced PICs in soleus in both young and older adults but had less effect in tibialis anterior in older adults. Our data suggest that older adults have preserved soleus PIC facilitation during lowintensity contractions, equivalent to activities such as standing and walking. However, a reduced reciprocal inhibition of PICs in tibialis anterior may contribute to locomotion impairments, such as increases in soleus-tibialis anterior co-activation during propulsion.
Bidirectional and reciprocal control of astrocyte free calcium by modest fluctuations in external potassium

Astrocytes sense and respond to changes in the concentration of extracellular K+, and separately contribute to multiple physiological processes through Ca2+ dependent mechanisms. Yet, whether a modest change in [K+]o impacts astrocyte free Ca2+ remains unclear. Using relative or quantitative two-photon fluorescence Ca2+ imaging in acute brain slices or in vivo in the somatosensory cortex from Sprague Dawley rats and C57Bl/6 mice, we showed that changes to external K+ (+/-1mM to 2.5mM) reciprocally controls the astrocyte Rhod-2 or OGB-1 Ca2+-dependent fluorescence in the soma, major processes and endfeet. The astrocyte Ca2+ decrease when [K+]o was elevated was sensitive to lowering the external concentration of Ca2+, Cl-, and HCO3-, but not Na+. Unexpectedly, the phenomenon was blocked by inhibiting K-Cl cotransport. Picrotoxin induced ictal neural activity drove an analogous decrease of astrocyte Ca2+. K+ mediated cerebral arteriole dilation in brain slices was also sensitive to inhibiting K-Cl cotransport as well as whole-cell patching a peri-arteriole astrocyte which perturbs normal Ca2+, Cl- and HCO3- concentration gradients. These data reveal subtle, bidirectional regulation of astrocyte free Ca2 via fluctuations of [K+]o within the physiological range.
Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought

Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used RNA-sequencing after ribosomal RNA depletion to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0. Concerning the changes detected in the organellar transcriptomes, chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Conversely, alternative splicing (AS) affected nearly 1,500 genes (9% of expressed nuclear genes). Of these, 42% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Moreover, we identified 927 isoform switching events. We provide a table of the most interesting candidates, and as proof of principle, increased drought tolerance of the carbonic anhydrase ca1 and ca2 mutants is shown. In addition, altering the relative contributions of the spliced isoforms could increase drought resistance. For example, our data suggest that the accumulation of a nonfunctional FLM (FLOWERING LOCUS M) isoform and not the ratio of FLM-ß and -δ isoforms may be responsible for the phenotype of early flowering under long-day drought conditions. In sum, our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought.
The genetic and environmental etiology of blood-based biomarkers related to risk of Alzheimer’s Disease in a population-based sample of early old-age men

The amyloid-tau-neurodegeneration (ATN) framework has led to an increased focus on Alzheimer’s disease (AD) biomarkers. The cost and invasiveness of obtaining biomarkers via cerebrospinal fluid has motivated efforts to develop sensitive blood-based biomarkers. Although AD is highly heritable, the biometric genetic and environmental etiology of blood-based biomarkers has never been explored. We therefore, analyzed plasma beta-amyloid (Aβ40, Aβ42, Aβ42/40), total tautau (t-tautau), and neurofilament light (NFL) biomarkers in a sample of 1,050 men aged 60 to 73 years (m=68.2, SD=2.5) from the Vietnam Era Twin Study of Aging (VETSA). Unlike Aβ and tautau, NFL does not define AD; however, as a biomarker of neurodegeneration it serves as the N component in the ATN framework. Univariate estimates suggest that familial aggregation in Aβ42, Aβ42/40, t-tau, and NFL is entirely explained by additive genetic influences accounting for 40%-58% of the total variance. All remaining variance is associated with unshared or unique environmental influences. For Aβ40, a additive genetic (31%), shared environmental (44%), and unshared environmental (25%) influences contribute to the total variance. In the more powerful multivariate analysis of Aβ42, Aβ40, t-tau, and NFL, heritability estimates range from 32% to 58%. Aβ40 and Aβ42 are statistically genetically identical (rg = 1.00, 95%CI = 0.92,1.00) and are also moderately environmentally correlated (re = 0.66, 95%CI = 0.59, 0.73). All other genetic and environmental associations were non-significant or small. Our results suggest that plasma biomarkers are heritable and that Aβ40 and Aβ42 share the same genetic influences, whereas the genetic influences on plasma t-tau and NFL are mostly unique and uncorrelated with plasma Aβ in early old-age men.
Hydrogen sulfide produced during fermentation improves ethanol production in Saccharomyces cerevisiae an evolutionarily conserved effect in other yeast species

Hydrogen sulfide (H2S) is a gas produced endogenously in organisms from the three domains of life. In mammals, it is involved diverse of physiological processes including regulation of blood pressure, and plays an important role in memory. In contrast, in unicellular organisms the physiological role of H2S has not been studied in detail. In yeast, for example, in the winemaking industry H2S is an undesirable byproduct because of its rotten egg smell, however its biological relevance has never been evaluated. The effect of H2S in cells is linked to a post-translational modification in cysteine residues known as S-persulfidation. We evaluated S-persulfidation in the Saccharomyces cerevisiae proteome. We screened S-persulfidated proteins from cells growing in fermentable carbon sources and we identified several glycolytic enzymes as S-persulfidation targets. Pyruvate kinase, catalyzing the last irreversible step of glycolysis, increases its activity in presence of a H2S donor. Yeast cells treated with H2S increased ethanol production; also, mutant cells that endogenously accumulate H2S produced more ethanol and ATP during the exponential growth phase. This mechanism of regulation of metabolism seems to be evolutionarily conserved in other yeast species because H2S induces ethanol production in the pre-Whole Genome Duplication Kluyveromyces marxianus and Meyerozyma guilliermondii. Our results suggest a new role of H2S in regulation of metabolism that could be useful for biotechnological applications.
Nuclear genetic diversity of head lice sheds light on human dispersal around the world

The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.
FPT algorithms for Token Jumping on Graphs

Suppose that we are given two independent sets I0 and Ir of a graph such that |I0| = |Ir |, and imagine that a token is placed on each vertex in I0. Then, the token jumping problem is to determine whether there exists a sequence of independent sets which transforms I0 into Ir so that each independent set in the sequence results from the previous one by moving exactly one token to another vertex. Therefore, all independent sets in the sequence must be of the same cardinality. This problem is W[1]-hard when parameterized only by the number of tokens. In this paper, we give FPT algorithms for general graphs when parameterized by both the number of tokens and the maximum degree.
Stability of SARS-CoV-2 in cold-chain transportation environments and the efficacy of disinfection measures

Cold-chain environment could extend the survival duration of SARS-CoV-2 and increases the risk of transmission. However, the effect of clod-chain environmental factors and packaging materials on SARS-CoV-2 stability and the efficacy of intervention measures to inactivate SARS-CoV-2 under cold-chain environment remains uncertain. This study aimed to unravel cold-chain environmental factors that preserved the stability of SARS-CoV-2 and disinfection measures against SARS-CoV-2 under the cold-chain environment. The spike gene of SARS-CoV-2 isolated from Wuhan hu-1 was used to construct the SARS-CoV-2 pseudovirus and used as model of the SARS-CoV-2 virus. The decay rate of SARS-CoV-2 pseudovirus in the cold-chain environment, various types of packaging material surfaces i.e., PE plastic, stainless steel, Teflon and cardboard, and in frozen seawater was investigated. The influence of LED visible light(wavelength 450 nm-780 nm) and airflow movement on the stability of SARS-CoV-2 pseudovirus at -18° C were subsequently assessed. The results show that SARS-CoV-2 pseudovirus decayed more rapidly on porous cardboard surface compared with the non-porous surfaces including PE plastic, stainless steel and Teflon. Compared with 25° C, the decay rate of SARS-CoV-2 pseudovirus was significantly lower at low temperature. Seawater preserved viral stability both at -18° C and repeated freeze-thawing cycles compared with deionized water. LED visible light illumination and airflow movement environment at -18° C reduced the SARS-CoV-2 pseudovirus stability. In conclusion, our results indicate cold-chain temperature and seawater as risk factors for SARS-CoV-2 transmission and LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment. Importance It is widely recognized that low temperature is a condition for maintaining virus vitality, and cold-chain transportation spreads the events of the SARS-CoV-2 were reported. This study provides that the decay rate of the SARS-CoV-2 pseudovirus at low temperatures varies on different packaging materials, and salt ions present in frozen foods such as seafood may protect virus survival. These results provide evidence for the possibility of SARS-CoV-2 transmission through cold-chain transport and also suggest the importance for disinfection of items. However, the commonly used disinfection methods of ultraviolet radiation and chemical reagents are generally not suitable for the disinfection of frozen food. Our study shows LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment. This has implications for reducing the long-distance transmission of the virus through cold-chain transportation.
On the Renyi entropy, Boltzmann Principle, Levy and power-law distributions and Renyi parameter

The Renyi entropy with a free Renyi parameter $q$ is the most justified form of information entropy, and the Tsallis entropy may be regarded as a linear approximation to the Renyi entropy when $q\simeq 1$. When $q\to 1$, both entropies go to the Boltzmann--Shannon entropy. The application of the principle of maximum of information entropy (MEP) to the Renyi entropy gives rise to the microcanonical (homogeneous) distribution for an isolated system. Whatever the value of the Renyi parameter $q$ is, in this case the Renyi entropy becomes the Boltzmann entropy $S_B=k_B\ln W$, that provides support for universality of the Boltzmann's principle of statistical mechanics. For a system being in contact with a heat bath, the application of MEP to the Renyi entropy gives rise to Levy distribution (or, $q$-distribution) accepted as one of the main results of the so-called nonextensive statistics. The same distribution is derived here for a small physical system experiencing temperature fluctuations. The long--range "tail" of the Levy distribution is the power--law (Zipf-Pareto) distribution with the exponent $s$ expressed via $q$. The exponent and free Renyi parameter $q$ can be uniquely determined with the use of a further extension of MEP. Then typical values of $s$ are found within the range $1.3÷2$ and of $q$ within the range $0.25÷0.5$, in dependence on parameters of stochastic systems.