Redundância funcional de plantas lenhosas residentes do subosque de dois fragmentos de Mata Atlântica

O desempenho dos organismos em determinada condição ambiental depende das estratégias ecológicas desenvolvidas ao longo da sua evolução, as quais são expressas por combinações de atributos funcionais (AF) que conferem vantagem adaptativa em um dado habitat. Este estudo avaliou o padrão de convergência funcional de espécies de subosque de duas comunidades vegetais de Mata Atlântica, Floresta Ombrófila Densa, no sul do Brasil. Para isso, foram amostradas 15 parcelas por fragmento de estudo, com seleção de 30 espécies nativas residentes de subosque que foram descritas a partir de 16 AF morfológicos, ecofisiológicos, fenológicos e reprodutivos. Radiação luminosa, conteúdo de matéria orgânica e umidade gravimétrica foram as variáveis ambientais mensuradas. A análise funcional das comunidades foi realizada por meio do software SYNCSA. Os AF que maximizam a convergência entre as espécies foram: folha simples, oposta e elíptica, a floração na primavera, a condição ciófita e secundária, a via fotossintética C3, a polinização melitofílica e a dispersão ornitocórica de frutos polispérmicos. As duas comunidades estudadas são medianamente redundantes funcionalmente devido à convergência de AF entre as espécies. A redundância funcional fornece resiliência a comunidade, em consequência das respostas compensatórias das espécies, o que reforça a importância da vegetação do subosque para a manutenção dos processos ecossistêmicos e a latente necessidade de inclusão das espécies desse estrato florestal em ações de restauração ambiental. Functional redundancy of woody plants resident in the understory of two fragments of the Atlantic Forest A B S T R A C TThe performance of organisms in each environmental condition is based on the ecological strategies developed throughout their evolution, expressed in combinations of functional traits (FA) which verifies adaptive advantage in each environment. The study evaluated the trait convergence assembly patterns of understory species in two plant communities of Atlantic Dense Forest in southern Brazil. To answer the question, 15 plots were sampled per fragment of study, with a selection of 30 native species of understory that were described by 16 morphological, ecophysiological, phenological and reproductive traits. Luminous radiation, organic matter content and gravimetric moisture were the environmental variables measured. The functional analysis of communities was measured using the software SYNCSA. The AF that maximized the convergence between species was: simple, opposite and elliptical leaf, flowering during the spring, cyophyte and secondary condition, photosynthesis c3, melitophilic pollination and ornithochoric dispersion of polyspermyc fruits. The two communities studied are moderately functionally redundant due to species functional convergence. Functional redundancy provides resilience to the community, as a result of species compensatory responses, which reinforces the importance of understory vegetation for the maintenance of ecosystem processes and the latent need for the inclusion of the understory species in restoration actions.Keywords: functional traits, functional convergence, ecological strategy, functional redundancy, resilience.

Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies

Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis.

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.

Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations

Different species can find convergent solutions to adapt their genome to the same evolutionary constraints, although functional convergence promoted by chromosomal rearrangements in different species has not previously been found. In this work, we discovered that two domesticated yeast species, Saccharomyces cerevisiae, and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentation environments. We found two new heterologous chromosomal translocations in fermentative strains of S. uvarum at the SSU1 locus, involved in sulfite resistance, an antimicrobial additive widely used in food production. These are convergent events that share similarities with other SSU1 locus chromosomal translocations previously described in domesticated S. cerevisiae strains. In S. uvarum, the newly described VIIXVI and XIXVI chromosomal translocation generate an overexpression of the SSU1 gene and confer increased sulfite resistance. This study highlights the relevance of chromosomal rearrangements to promote the adaptation of yeast to anthropic environments.

Exploring the miRNA-mediated response to combined stresses in melon plants

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop-productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of melon response to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress-combinations, most interactions were negative suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling evidences that the response to combined stresses cannot be easily predicted from the study individual stresses

Characterization of Generalized Young Measures Generated by $${\mathcal {A}}$$-free Measures

We give two characterizations, one for the class of generalized Young measures generated by $${{\,\mathrm{{\mathcal {A}}}\,}}$$ A -free measures and one for the class generated by $${\mathcal {B}}$$ B -gradient measures $${\mathcal {B}}u$$ B u . Here, $${{\,\mathrm{{\mathcal {A}}}\,}}$$ A and $${\mathcal {B}}$$ B are linear homogeneous operators of arbitrary order, which we assume satisfy the constant rank property. The first characterization places the class of generalized $${\mathcal {A}}$$ A -free Young measures in duality with the class of $${{\,\mathrm{{\mathcal {A}}}\,}}$$ A -quasiconvex integrands by means of a well-known Hahn–Banach separation property. The second characterization establishes a similar statement for generalized $${\mathcal {B}}$$ B -gradient Young measures. Concerning applications, we discuss several examples that showcase the failure of $$\mathrm {L}^1$$ L 1 -compensated compactness when concentration of mass is allowed. These include the failure of $$\mathrm {L}^1$$ L 1 -estimates for elliptic systems and the lack of rigidity for a version of the two-state problem. As a byproduct of our techniques we also show that, for any bounded open set $$\Omega $$ Ω , the inclusions $$\begin{aligned} \mathrm {L}^1(\Omega ) \cap \ker {\mathcal {A}}&\hookrightarrow {\mathcal {M}}(\Omega ) \cap \ker {{\,\mathrm{{\mathcal {A}}}\,}}\,,\\ \{{\mathcal {B}}u\in \mathrm {C}^\infty (\Omega )\}&\hookrightarrow \{{\mathcal {B}}u\in {\mathcal {M}}(\Omega )\} \end{aligned}$$ L 1 ( Ω ) ∩ ker A ↪ M ( Ω ) ∩ ker A , { B u ∈ C ∞ ( Ω ) } ↪ { B u ∈ M ( Ω ) } are dense with respect to the area-functional convergence of measures.

Current Knowledge of Endolysosomal and Autophagy Defects in Hereditary Spastic Paraplegia

Hereditary spastic paraplegia (HSP) refers to a group of neurological disorders involving the degeneration of motor neurons. Due to their clinical and genetic heterogeneity, finding common effective therapeutics is difficult. Therefore, a better understanding of the common pathological mechanisms is necessary. The role of several HSP genes/proteins is linked to the endolysosomal and autophagic pathways, suggesting a functional convergence. Furthermore, impairment of these pathways is particularly interesting since it has been linked to other neurodegenerative diseases, which would suggest that the nervous system is particularly sensitive to the disruption of the endolysosomal and autophagic systems. In this review, we will summarize the involvement of HSP proteins in the endolysosomal and autophagic pathways in order to clarify their functioning and decipher some of the pathological mechanisms leading to HSP.