Metabolic flexibility determines human NK cell functional fate in the tumor microenvironment

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Carcass Persistence and Detectability: Reducing the Uncertainty Surrounding Wildlife-Vehicle Collision Surveys

Carcass persistence time and detectability are two main sources of uncertainty on roadkill surveys. In this study, we evaluate the influence of these uncertainties on roadkill surveys and estimates. To estimate carcass persistence time, three observers (including the driver) surveyed 114km by car on a monthly basis for two years, searching for wildlife-vehicle collisions (WVC). Each survey consisted of five consecutive days. To estimate carcass detectability, we randomly selected stretches of 500m to be also surveyed on foot by two other observers (total 292 walked stretches, 146 km walked). We expected that body size of the carcass, road type, presence of scavengers and weather conditions to be the main drivers influencing the carcass persistence times, but their relative importance was unknown. We also expected detectability to be highly dependent on body size. Overall, we recorded low median persistence times (one day) and low detectability (<10%) for all vertebrates. The results indicate that body size and landscape cover (as a surrogate of scavengers’ presence) are the major drivers of carcass persistence. Detectability was lower for animals with body mass less than 100g when compared to carcass with higher body mass. We estimated that our recorded mortality rates underestimated actual values of mortality by 2–10 fold. Although persistence times were similar to previous studies, the detectability rates here described are very different from previous studies. The results suggest that detectability is the main source of bias across WVC studies. Therefore, more than persistence times, studies should carefully account for differing detectability when comparing WVC studies.     

Synchronisation and stability in river metapopulation networks

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability – conferred by fluctuation and synchronisation dampening – emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations.     

Investigating aerial diversity of non-fungal eukaryotes across a 40° latitudinal transect using DNA metabarcoding

The high number of bipolar and widespread bryophyte and microbial taxa in the Antarctic flora suggests the effective Long-Distance Dispersal (LDD) of spores and other propagules from lower latitudes and even the Northern Hemisphere to Antarctica and the sub-Antarctic regions. However, few studies have attempted to document the transfer mechanisms by which potential newcomers may arrive in Antarctica. Commonly suggested or assumed mechanisms include transport in air currents, adventitious transfer with migrating or vagrant birds, and with human assistance. In this study, we investigated the biodiversity present in the air along a 40° latitudinal transect, from the port city of Rio de Janeiro, Brazil (ca. 22°S) to Comandante Ferraz Station on King George Island (South Shetland Islands, ca. 62°S), maritime Antarctica, to shed light on the potential role of LDD in species distribution. Air samples were collected in October 2021 on the Brazilian polar support vessel Ary Rongel using air filters with membranes of 0.22 μm. Total DNA was extracted from the filters and the Internal Transcribed Spacer (ITS2) DNA sequence was used for metabarcoding. A total of 53 non-fungal taxa representing three kingdoms (most abundantly Viridiplantae) and six phyla (most abundantly Bryophyta and Magnoliophyta) were assigned from the sequences found. Aerial biodiversity was greater closer to the coast and generally decreased with increasing latitude, although a small increase was apparent in the South Shetland Islands. The taxa assigned are generally present in coastal biomes, although a small proportion of the assignments represented taxa of more distant origin, supporting the occurrence of LDD in the air column.     

Diversity in the genus Rhabdias (Nematoda,Rhabdiasidae): Evidence for cryptic speciation

Lungworms from the genus Rhabdias are common parasites of amphibians and reptiles distributed worldwide. To assess the diversity of Rhabdias spp., we performed molecular analyses of 35 specimens sampled in different regions of Brazil. Molecular analyses were based on the internal transcribed spacer (ITS), large subunit (28S) ribosomal and the cytochrome oxidase I (COI) mitochondrial genes. DNA sequence divergence was compared among ribosomal and mitochondrial genes, analyses using the general mixed Yule‐coalescent (GMYC) method based on the COI gene were used to identify possible cryptic diversity, and phylogenetic analyses using concatenated ITS and 28S ribosomal genes were used to test the monophyly of Rhabdiasidae. We revealed five morphospecies: R. cf. stenocephala, R. breviensis, R. pseudosphaerocephala and two new species, Rhabdias sp.4 and Rhabdias sp.5. DNA sequence levels of divergence among genes ITS, 28S and COI were compared, and the efficiency of the molecular markers to identify species (ITS and COI) and lineages (COI) was tested. GMYC was assigned to 17 well‐supported clades (i.e., 17 species), and cryptic diversity was detected in the Neotropical region as evidenced by the multiple lineages in R. breviensis and R. pseudosphaerocephala. In addition, our results suggest evidence for host–parasite cophylogeny in the R. pseudosphaerocephala complex and dispersal events among their populations. Phylogenetic analyses supported the monophyly of Rhabdiasidae and improved the resolution of main clades. Rhabdias breviensis is closely related to Rhabdias cf. africanus, Rhabdias cf. stenocephala, R. pseudosphaerocephala, Rhabdias sp.4 and Rhabdias sp.5 grouping together in a main clade with Neotropical‐related species. The large geographical distribution appeared to be a phylogenetic pattern among the species of Rhabdias from the neotropics.     

Solution structures of tetrahaem ferricytochrome c3 from Desulfovibrio vulgaris (Hildenborough) and its K45Q mutant: The molecular basis of cooperativity

The NMR structure of the oxidised wild-type cytochrome c₃ from Desulfovibrio vulgaris Hildenborough was determined in solution. Using a newly developed methodology, NMR data from the K45Q mutant was then grafted onto data from the wild-type protein to determine the structure in the region of the mutation. The structural origins of the redox-Bohr effect and haem-haem cooperativities are discussed with respect to the redox-related conformational changes observed in solution.     

Accuracy and Reliability of Severity Estimates Using Linear or Logarithmic Disease Diagram Sets in True Colour or Black and White: a Study Case for Rice Brown Spot

Four disease diagram sets to aid in assessments of rice brown spot severity were developed and evaluated with regard to accuracy and reliability of the estimates. These sets had severity increments in a linear (LIN) or logarithmic (LOG) fashion with the diagrams depicted in true colour (COL) or black and white (BW). Ten inexperienced raters evaluated one of the sets, totalling forty raters. On each group of raters, the assessment was made first unaided and then aided with the respective diagram set. The minimum and the maximum severities of the diagram sets were 0.5 and 36%, respectively, and the five intermediate severity values were 6, 12, 18, 24 and 32% for the LIN diagram sets, and 1.8, 3.3, 6, 11 and 20% for the LOG sets. Overall agreement, measured by the Lin's concordance correlation coefficient (ρ_c), increased considerably when using the aid (unaided mean ρ_c = 0.53, aided mean ρ_c = 0.87) due to a strong reduction in the systematic bias, measured by the bias correction factor C_b (unaided mean C_b = 0.60, aided mean C_b = 0.95). All diagrams led to similar accuracy and precision, but a consistent overestimation was still observed when using the LIN sets, and variability for the absolute errors was higher for the LOG sets, compared with the LIN sets. Estimates using the diagram sets were more reliable based on the intraclass correlation (mean ρ = 0.79–0.86) compared with unaided estimates (mean ρ = 0.51–0.67). Raters exhibited preference for specific values, such as the ‘knots’ (10, 20, 30%, etc.), and the severity values represented in the diagrams, especially when using the LIN sets. The diagram sets similarly helped to improve accuracy and reliability of estimates of rice brown spot epidemics.