Miracle-dz/UniFAR-FTUs huggingface dataset:
New handbook for standardised measurement of plant functional traits worldwide

Plant functional traits are the features (morphological, physiological, phenological) that represent ecological strategies and determine how plants respond to environmental factors, affect other trophic levels and influence ecosystem properties. Variation in plant functional traits, and trait syndromes, has proven useful for tackling many important ecological questions at a range of scales, giving rise to a demand for standardised ways to measure ecologically meaningful plant traits. This line of research has been among the most fruitful avenues for understanding ecological and evolutionary patterns and processes. It also has the potential both to build a predictive set of local, regional and global relationships between plants and environment and to quantify a wide range of natural and human-driven processes, including changes in biodiversity, the impacts of species invasions, alterations in biogeochemical processes and vegetation–atmosphere interactions. The importance of these topics dictates the urgent need for more and better data, and increases the value of standardised protocols for quantifying trait variation of different species, in particular for traits with power to predict plant- and ecosystem-level processes, and for traits that can be measured relatively easily. Updated and expanded from the widely used previous version, this handbook retains the focus on clearly presented, widely applicable, step-by-step recipes, with a minimum of text on theory, and not only includes updated methods for the traits previously covered, but also introduces many new protocols for further traits. This new handbook has a better balance between whole-plant traits, leaf traits, root and stem traits and regenerative traits, and puts particular emphasis on traits important for predicting species’ effects on key ecosystem properties. We hope this new handbook becomes a standard companion in local and global efforts to learn about the responses and impacts of different plant species with respect to environmental changes in the present, past and future.
Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2

Hydroxychloroquine, used to treat malaria and some autoimmune disorders, potently inhibits viral infection of SARS coronavirus (SARS-CoV-1) and SARS-CoV-2 in cell-culture studies. However, human clinical trials of hydroxychloroquine failed to establish its usefulness as treatment for COVID-19. This compound is known to interfere with endosomal acidification necessary to the proteolytic activity of cathepsins. Following receptor binding and endocytosis, cathepsin L can cleave the SARS-CoV-1 and SARS-CoV-2 spike (S) proteins, thereby activating membrane fusion for cell entry. The plasma membrane-associated protease TMPRSS2 can similarly cleave these S proteins and activate viral entry at the cell surface. Here we show that the SARS-CoV-2 entry process is more dependent than that of SARS-CoV-1 on TMPRSS2 expression. This difference can be reversed when the furin-cleavage site of the SARS-CoV-2 S protein is ablated. We also show that hydroxychloroquine efficiently blocks viral entry mediated by cathepsin L, but not by TMPRSS2, and that a combination of hydroxychloroquine and a clinically-tested TMPRSS2 inhibitor prevents SARS-CoV-2 infection more potently than either drug alone. These studies identify functional differences between SARS-CoV-1 and -2 entry processes, and provide a mechanistic explanation for the limited in vivo utility of hydroxychloroquine as a treatment for COVID-19. Author Summary The novel pathogenic coronavirus SARS-CoV-2 causes COVID-19 and remains a threat to global public health. Chloroquine and hydroxychloroquine have been shown to prevent viral infection in cell-culture systems, but human clinical trials did not observe a significant improvement in COVID-19 patients treated with these compounds. Here we show that hydroxychloroquine interferes with only one of two somewhat redundant pathways by which the SARS-CoV-2 spike (S) protein is activated to mediate infection. The first pathway is dependent on the endosomal protease cathepsin L and sensitive to hydroxychloroquine, whereas the second pathway is dependent on TMPRSS2, which is unaffected by this compound. We further show that SARS-CoV-2 is more reliant than SARS coronavirus (SARS-CoV-1) on the TMPRSS2 pathway, and that this difference is due to a furin cleavage site present in the SARS-CoV-2 S protein. Finally, we show that combinations of hydroxychloroquine and a clinically tested TMPRSS2 inhibitor work together to effectively inhibit SARS-CoV-2 entry. Thus TMPRSS2 expression on physiologically relevant SARS-CoV-2 target cells may bypass the antiviral activities of hydroxychloroquine, and explain its lack of in vivo efficacy.
Microzooplankton Grazing in the Southern Ocean: Implications for the Carbon Cycle

Microzooplankton grazing and protozooplankton community structure was investigated in austral summer (Jan./Feb.) and winter (June/July) 1993 in the Atlantic sector of the Southern Ocean during the SAAMES (South African Antarctic Marine Ecosystem Study) Il and III cruises. Grazing was estimated at 22 stations in summer and at 15 stations in winter by employing the sequential dilution technique. Nano-heterotrophic flagellates (< 20 μm) and ciliates (aloricate ciliates and tintinnids) dominated the protozooplankton assemblages along both transects. Densities in winter were, however, nearly an order of magnitude lower than in summer. Microzooplankton grazing removed between 0 and 28% (mean = 13.2%) of the initial phytoplankton stock in summer and, between 24 and 51 % of the initial stock (mean = 37.6%) in winter. The potential primary production removed during summer ranged between 0 and 46% (mean = 22.0%) compared with the winter range of 56–83% (mean = 67.2%). Size selectivity grazing experiments conducted during both studies suggest that microzooplankton preferentially graze on the nano- (20–2.0μm) and picophytoplankton (2.0–0.2μm) size fractions. These results have important implications for the efficiency of the carbon pump in the Southern Ocean. During summer when the larger cells dominate phytoplankton biomass, the bulk of the photosynthetically fixed carbon appears to be channelled to the meso- and macrozooplankton fractions. This results in a rapid transfer of organic carbon out of the zone of regeneration to the deep ocean via vertical migration and large faecal pellet production. During winter, however, an increase in the contribution of the smaller size fractions to total phytoplankton biomass results in a greater proportion of the photosynthetically fixed carbon being channelled to the microzooplankton fraction. The efficiency of the carbon pump is, therefore, reduced in that the transfer of carbon below the zone of regeneration is reduced as carbon is recycled mostly within the microbial loop in the upper mixed layer.
The BMP antagonist gremlin 1 contributes to the development of cortical excitatory neurons, motor balance and fear responses

Bone morphogenetic protein (BMP) signaling is required for early forebrain development and cortical formation. How the endogenous modulators of BMP signaling regulate the structural and functional maturation of the developing brain remains unclear. Here we show that expression of the BMP antagonist, Grem1, marks a neuroprogenitor that gives rise to layer V and VI glutamatergic neurons in the embryonic mouse brain. Lineage tracing of Grem1-expressing cells in the embryonic brain was examined by administration of tamoxifen to pregnant Grem1creERT Rosa26LSLTdtomato mice at 13.5 days post coitum (dpc), followed by collection of embryos later in gestation. In addition, at 14.5 dpc, bulk mRNA seq analysis of differentially expressed transcripts between FACS sorted Grem1 positive and negative cells was performed. We also generated Emx1-cre mediated Grem1 conditional knockout mice (Emx1-Cre;Grem1flox/flox) in which the Grem1 gene was deleted specifically in the dorsal telencephalon. Grem1Emx1cKO animals had reduced cortical thickness, especially layers V and VI and impaired motor balance and fear sensitivity compared to littermate controls. This study has revealed new roles for Grem1 in the structural and functional maturation of the developing cortex. Summary statement The BMP antagonist, Grem1, marks neuroprogenitors that give rise to deep layer glutamatergic neurons in the embryonic mouse brain. Grem1 conditional knockout mice display cortical and behavioural abnormalities.
Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity

Significance Humans and our close evolutionary relatives respond differently to a large number of infections. Such differences are thought to result, at least in part, from interspecies differences in immune function. Here, we report on the whole-genome expression of blood leukocytes from four primate species responding to bacterial and viral stimulation. We show that apes mount a markedly stronger early transcriptional response to both viral and bacterial stimulation when compared to African and Asian monkeys. In addition, our findings suggest that apes activate a broader array of defense molecules that may be beneficial for early pathogen killing at the potential cost of increased energy expenditure and tissue damage. Our results provide insight into the evolution of immune responses in primates. Despite their close genetic relatedness, apes and African and Asian monkeys (AAMs) differ in their susceptibility to severe bacterial and viral infections that are important causes of human disease. Such differences between humans and other primates are thought to be a result, at least in part, of interspecies differences in immune response to infection. However, because of the lack of comparative functional data across species, it remains unclear in what ways the immune systems of humans and other primates differ. Here, we report the whole-genome transcriptomic responses of ape species (human and chimpanzee) and AAMs (rhesus macaque and baboon) to bacterial and viral stimulation. We find stark differences in the responsiveness of these groups, with apes mounting a markedly stronger early transcriptional response to both viral and bacterial stimulation, altering the transcription of ∼40% more genes than AAMs. Additionally, we find that genes involved in the regulation of inflammatory and interferon responses show the most divergent early transcriptional responses across primates and that this divergence is attenuated over time. Finally, we find that relative to AAMs, apes engage a much less specific immune response to different classes of pathogens during the early hours of infection, up-regulating genes typical of anti-viral and anti-bacterial responses regardless of the nature of the stimulus. Overall, these findings suggest apes exhibit increased sensitivity to bacterial and viral immune stimulation, activating a broader array of defense molecules that may be beneficial for early pathogen killing at the potential cost of increased energy expenditure and tissue damage.
Mycorrhizal symbiosis alleviates plant drought stress within and across plant generations via plasticity

Phenotypic plasticity is essential for organisms to adapt to local ecological conditions. Little is known about how mutualistic interactions, such as arbuscular mycorrhizal (AM) symbiosis, mediate plant phenotypic plasticity and to what extent this plasticity may be heritable (i.e. transgenerational effects). We tested for plant plasticity within- and across-generations in response to AM symbiosis and varying water availability in a full factorial experiment over two generations, using the perennial apomictic herb Taraxacum brevicorniculatum. We examined changes in phenotype, performance, and AM fungal colonization of the offspring throughout plant development. AM symbiosis and water availability triggered phenotypic changes during the life cycle of plants. Additionally, both triggered adaptive transgenerational effects, especially detectable during the juvenile stage. Drought stress and absence of AM fungi caused concordant plant phenotypic modifications towards a “stress-coping phenotype” within-and across-generations. Offspring’s AM fungal colonization was also affected by the parental environment. AM symbiosis can trigger transgenerational effects, including changes in functional traits related to resource-use acquisition and AM fungal colonization of the offspring, in turn affecting the biotic interaction. Thus, transgenerational effects of mycorrhizal symbiosis are not limited to plant fitness, but also improve plants’ ability to cope with environmental stress.
Purkinje Cell-Specific Knockout of Tyrosine Hydroxylase Impairs Cognitive Behaviors

Tyrosine hydroxylase (Th) expression has previously been reported in Purkinje cells (PCs) of rodents and humans, but its role in the regulation of behavior is not understood. Catecholamines are well known for facilitating cognitive behaviors and are expressed in many regions of the brain. Here, we investigated a possible role in cognitive behaviors of PC catecholamines, by mapping and testing functional roles of Th positive PCs in mice. Comprehensive mapping analyses revealed a distinct population of Th expressing PCs primarily in the posterior and lateral regions of the cerebellum (comprising about 18% of all PCs). To identify the role of PC catecholamines, we selectively knocked out Th in PCs using a conditional knockout approach, by crossing a Purkinje cell-selective Cre recombinase line, Pcp2-Cre, with a floxed tyrosine hydroxylase mouse line (Thlox/lox) to produce Pcp2-Cre;Thlox/lox mice. This manipulation resulted in approximately 50% reduction of Th protein expression in the cerebellar cortex and lateral cerebellar nucleus, but no reduction of Th in the locus coeruleus, which is known to innervate the cerebellum in mice. Pcp2-Cre;Thlox/lox mice showed impairments in behavioral flexibility, response inhibition, social recognition memory, and associative fear learning relative to littermate controls, but no deficits in gross motor, sensory, instrumental learning, or sensorimotor gating functions. Catecholamines derived from specific populations of PCs appear to support cognitive functions, and their spatial distribution in the cerebellum suggests that they may underlie patterns of activation seen in human studies on the cerebellar role in cognitive function.
High neutralizing potency of swine glyco-humanized polyclonal antibodies against SARS-CoV-2

Perfusion of convalescent plasma (CP) has demonstrated a potential to improve the pneumonia induced by SARS-CoV-2, but procurement and standardization of CP are barriers to its wide usage. Many monoclonal antibodies (mAbs) have been developed but appear insufficient to neutralize SARS-CoV-2 unless two or three of them are being combined. Therefore, heterologous polyclonal antibodies of animal origin, that have been used for decades to fight against infectious agents might represent a highly efficient alternative to the use of CP or mAbs in COVID-19 by targeting multiple antigen epitopes. However, conventional heterologous polyclonal antibodies trigger human natural xenogeneic antibody responses particularly directed against animal-type carbohydrate epitopes, mainly the N-glycolyl form of the neuraminic acid (Neu5Gc) and the Gal α1,3-galactose (αGal), ultimately forming immune complexes and potentially leading to serum sickness or allergy. To circumvent these drawbacks, we engineered animals lacking the genes coding for the cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) and α1,3-galactosyl-transferase (GGTA1) enzymes to produce glyco-humanized polyclonal antibodies (GH-pAb) lacking Neu5Gc and α-Gal epitopes. We found that pig IgG Fc domains fail to interact with human Fc receptors and thereby should confer the safety advantage to avoiding macrophage dependent exacerbated inflammatory responses, a drawback possibly associated with antibody responses against SARS-CoV-2 or to avoiding a possible antibody-dependent enhancement (ADE). Therefore, we immunized CMAH/GGTA1 double knockout (DKO) pigs with the SARS-CoV-2 spike receptor-binding domain (RBD) to elicit neutralizing antibodies. Animals rapidly developed a hyperimmune response with anti-SARS-CoV-2 end-titers binding dilutions over one to a million and end-titers neutralizing dilutions of 1:10,000. The IgG fraction purified and formulated following clinical Good Manufacturing Practices, named XAV-19, neutralized Spike/angiotensin converting enzyme-2 (ACE-2) interaction at a concentration < 1μg/mL and inhibited infection of human cells by SARS-CoV-2 in cytopathic assays. These data and the accumulating safety advantages of using glyco-humanized swine antibodies in humans warranted clinical assessment of XAV-19 to fight against COVID-19.
Island ecology and contingent theory: the role of spatial scale and taxonomic bias

Scale, the scale dependency of patterns and processes, and the ways that organisms scale their responses to these patterns and processes are central to island and landscape ecology. Here, we take a database of studies in island ecology and investigate how studies have changed over a 40-year period with respect to spatial scale and organisms studied. We demonstrate that there have been changes in the spatial scale of islands studied and that there is taxonomic bias in favour of vertebrates in island ecological studies when compared to scientific publications as a whole. We discuss how such taxonomic bias may have arisen and discuss the implications for ecology and biogeography.
The Evolution of the Sperm Transport Complex in Male Plethodontid Salamanders (Amphibia, Urodela, Plethodontidae)

Based on previous literature, male salamanders of the genus Eurycea possess sperm transport ducts that are homogenous (in terms of histology) along their entire length; i.e., a transverse tubule. Considering this structural homogeneity is unique among salamanders, this feature could potentially be a synapomorphy for Spelerpinae. We tested this hypothesis by re-evaluating the histology of the sperm transport ducts of multiple members of Spelerpinae (Eurycea longicauda, E. lucifuga, and E. multiplicata) and compared our results with representatives from all subfamilies of Plethodontidae (Bolitoglossinae, Hemidactylinae, and Plethodontinae). We reject the findings of previous work that spelerpine salamanders possess homogenous sperm transport ducts along their entire length. Discrete regions are present along the sperm transport ducts of Spelerpinae that include, from proximal to distal, a vas efferens, genital kidney proximal tubule, genital kidney distal tubule, and genital kidney collecting tubule. A distinct renal corpuscle often exists between the communication of the vas efferens and genital kidney proximal tubule. This regionality is not only stereotypical for the sperm transport ducts in all plethodontid salamanders, but also for salamanders in general. Similar to other lineages of salamanders (i.e., Rhyacotritonidae and Sirenidae), all plethodontid salamanders examined lack a longitudinal collecting duct and distinct neck and intermediate segments. We found no characteristic that could potentially serve as a non-ambiguous synapomorphy for Spelerpinae or Plethodontidae with use of sperm transport duct histology. However, it appears that the Bolitoglossinae, Hemidactylinae, and Spelerpinae often lack arteriole connection to their glomeruli within the genital kidney renal corpuscles, yet this trait is ambiguous within taxa of these subfamilies.
Ideal pear sensory attributes and fruit characteristics

The relationship between the objective assessment of sensory attributes or fruit characteristics of pear (Pyrus communis L.) fruit and the corresponding consumer or sensory panel rating was studied. Optimum fruit diameter was between 6 and 7.5 cm. Some fruit were judged to be too large. Fruit with a bright yellow skin were rated ideal, whereas green or red skin was rated less favorably. A pyriform shape with a length : diameter ratio range of 1.44 to 1.48 was optimum. Round fruit or very elongated fruit were considered undesirable. Perceived firmness increased linearly as the measured firmness increased, with the optimum firmness at 27 to 30 N (using an 11.1-mm penetrometer tip). Perceived juiciness was negatively, linearly related to measured firmness. Ideal firmness for an ideal juiciness rating was 18 to 22 N. Acceptable soluble solids concentrations (SSC) varied with the study year, but ranged between 13.6% and 17.2%. The sweet/sour balance (ratio of SSC : titratable acidity) was a useful indicator of fruit quality.
The Geographic Distribution of Big Five Personality Traits

The Big Five Inventory (BFI) is a self-report measure designed to assess the high-order personality traits of Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness. As part of the International Sexuality Description Project, the BFI was translated from English into 28 languages and administered to 17,837 individuals from 56 nations. The resulting cross-cultural data set was used to address three main questions: Does the factor structure of the English BFI fully replicate across cultures? How valid are the BFI trait profiles of individual nations? And how are personality traits distributed throughout the world? The five-dimensional structure was robust across major regions of the world. Trait levels were related in predictable ways to self-esteem, sociosexuality, and national personality profiles. People from the geographic regions of South America and East Asia were significantly different in openness from those inhabiting other world regions. The discussion focuses on limitations of the current data set and important directions for future research.
The Law and Ethics of Female Genital Cutting

In this chapter, we contrast legal and ethical perspectives on two forms of nontherapeutic female genital cutting: those commonly known as “female genital mutilation” and those commonly known as “female genital cosmetic surgeries. ” We begin by questioning the usefulness of these categories—and the presumed distinctions upon which they rest—stressing the shared features of the two sets of practices. Taking UK legislation as a case study, we show that there are troubling inconsistencies in the way in which female genital cutting is understood in Western contexts. Specifically: (a) all nontherapeutic genital alterations to female minors are criminalised, typically with harsh penalties for transgressing the law, while even more invasive nontherapeutic genital alterations to male and intersex minors are permitted and almost entirely unregulated; and (b) genital alterations of adult women regarded as “cosmetic” in nature are treated as legal, while in some jurisdictions, anatomically identical procedures classified as “mutilation” are illegal. This chapter highlights these and other inconsistencies, speculates as to why they arise in Western contexts, and explores the scope for more consistent and constructive attitudes and legislation.