In The Presence Of Absence
Spanning more than 14 rooms and work by 23 artists and artist collectives, the interdisciplinary exhibition In the Presence of Absence presents a selection of (counter) narratives that challenge fixed ideas about our society and question how history is written. When not addressed by organizations such as schools, libraries, archives, and museums, the absence of these stories forms knowledge gaps within the public debates that shape our collective consciousness and memory.
In the presence of absence
The title of the exhibition is inspired by the title of the last book written by the poet Mahmoud Darwish. In the context of this exhibition, the presence of absence" emphasizes how stories function and resonate within a society.
As other arbuscular mycorrhizal fungi, Gigaspora margarita contains unculturable endobacteria in its cytoplasm. A cured fungal line has been obtained and showed it was capable of establishing a successful mycorrhizal colonization. However, previous OMICs and physiological analyses have demonstrated that the cured fungus is impaired in some functions during the pre-symbiotic phase, leading to a lower respiration activity, lower ATP, and antioxidant production. Here, by combining deep dual-mRNA sequencing and proteomics applied to Lotus japonicus roots colonized by the fungal line with bacteria (B+) and by the cured line (B-), we tested the hypothesis that L. japonicus (i) activates its symbiotic pathways irrespective of the presence or absence of the endobacterium, but (ii) perceives the two fungal lines as different physiological entities. Morphological observations confirmed the absence of clear endobacteria-dependent changes in the mycorrhizal phenotype of L. japonicus, while transcript and proteomic datasets revealed activation of the most important symbiotic pathways. They included the iconic nutrient transport and some less-investigated pathways, such as phenylpropanoid biosynthesis. However, significant differences between the mycorrhizal B+/B- plants emerged in the respiratory pathways and lipid biosynthesis. In both cases, the roots colonized by the cured line revealed a reduced capacity to activate genes involved in antioxidant metabolism, as well as the early biosynthetic steps of the symbiotic lipids, which are directed towards the fungus. Similar to its pre-symbiotic phase, the intraradical fungus revealed transcripts related to mitochondrial activity, which were downregulated in the cured line, as well as perturbation in lipid biosynthesis.
A "Presence/Absence" LOI identifies whether any freshwater wetlands, State open waters or transition areas exist on a site, or on a portion of a site (See "Footprint of Disturbance" below) one acre or less. A presence/absence LOI also provides the resource value classification for any wetlands on the site.
A presence/absence LOI does not identify the boundaries or location of any freshwater wetlands, transition areas, and/or State open waters found within a site or portion thereof. To obtain an LOI indicating the location or the boundaries of freshwater wetlands, transition areas, and/or State open waters, an applicant must apply for a Line Delineation LOI (See the Delineation tab) for sites of up to an acre, or a line verification LOI (See the Verification tab) for sites over an acre.
The Department can issue a presence/absence LOI for any site, regardless of its size. Please see N.J.A.C. 7:7A-4.3, Presence/absence LOI, for the relevant section of the rules Application requirements for a LOI can be found in the "Freshwater Wetlands" tab of the "Forms, Checklists and Other Documents" webpage and at N.J.A.C. 7:7A-16.3.
Please see N.J.A.C. 7:7A-4.3, Presence/absence LOI, and specifically N.J.A.C. 7:7A-4.3(c) and (d), for the relevant rule provisions. Application requirements for a LOI can be found in the "Freshwater Wetlands" tab of the "Forms, Checklists and Other Documents" webpage and at N.J.A.C. 7:7A-16.3.
If we examine images captured from the off-axis Spot Light and Coaxial Ring Light geometries, we can visually determine the presence of the scoop, but neither image is particularly appropriate for a vision system inspection (Figs 2a & 2b). This circumstance is primarily the result of differential reflectivity from the metal can interior and the plastic scoop, along with the lack of light uniformity, incident on all the surfaces.
We focused on single-copy genes that have evolved under functional constraint for three reasons. First, this strategy simplified the analysis. When multiple-copy genes are similar to each other, reads from these genes are mapped to all genes with high similarity. Therefore, it is difficult to detect the absence of a multi-copy gene. Second, this strategy avoids the influence of functional compensation. For multi-copy genes, if one gene copy is absent, another gene with high similarity may compensate for the loss. In this case, the effect of the absence of a gene may be smaller than that of a single-copy gene. Third, gene annotation generally includes mis-annotation of genes due to gene prediction. To avoid using mis-annotated genes, we used genes that have evolved under functional constraint.
We detected PAPs in approximately 5% of single-copy genes. More than half of the PAP genes detected were specific to cnidarian lineages or Acroporidae or Acropora. Among all PAP genes in the genome assembly, roughly half were expressed in adults and/or larvae, and these expressed genes were differentially expressed among individuals depending on their presence or absence status. We also analyzed A. tenuis, the basal lineage in the genus Acropora [14, 15], and found that PAPs are a common genomic trait in A. tenuis, suggesting that PAPs may be a general feature among the genomes of species in the genus Acropora.
Next, we analyzed whether these shared PAPs were present in the common ancestor of Acropora species or if such events occurred independently. We determined the sequences at the boundary positions of an absence region in one PAP (LOC107329813) from A. digitifera and A. tenuis. The boundary positions for the two species were nearly identical (Fig. 1b; Additional file 1: Figure S2e and f), indicating a common ancestral origin of this PAP. In this analysis, we used only one PAP gene region. Therefore, to reveal the proportion of PAP genes that originated from the common ancestor of Acropora species, further analyses using large numbers of PAP loci are required.
We considered the potential deleterious effects of PAPs observed in this study. However, we found evidence suggesting that the absence of alleles is not highly deleterious. First, our samples and sequence data from the published database [16] were obtained from adult individuals; these individuals developed without serious defects, suggesting that the homozygous absence of these alleles was not lethal. Second, the frequencies of the homozygous absence allele were relatively high in PAPs. Among 516 PAP genes, 414 exhibited a homozygous absence in two or more individuals out of 33 total individuals. Third, the polymorphic state of over half of the PAP genes was shared among two subpopulations. If the homozygous absence was deleterious, individuals lacking both copies should be removed from the population by purifying selection, minimizing shared PAPs among populations. Accordingly, we concluded that most PAPs were not deleterious or were only slightly deleterious.
A. tenuis is located at the basal position in the genus Acropora [14, 15]. At least 17% of A. digitifera PAP genes were also PAPs in A. tenuis, suggesting that these PAPs are a general genomic characteristic in the genus Acropora, though the PAPs were only analyzed in two species belonging to the genus. For one gene, the boundaries of presence and absence alleles were nearly identical in these two species, indicating a single origin of the absence allele and the persistence of the PAP during the evolution of the genus Acropora. This analysis of boundary positions was limited to a single gene owing to gaps in the reference genome, the long length of deleted regions, and genetic divergence between species. Therefore, we could not rule out the possibility of independent acquisitions of other PAPs in A. tenuis.
2.We first used 391 incidental sightings of sambar deer and 12 biophysical variables to construct a presence-only habitat suitability model using Maxent. We then used that model to stratify field sampling, with proportionately greater sampling of cells with high predicted habitat suitability. Field sampling, consisting of faecal pellet surveys, sign surveys and camera trapping, was conducted in 80 4-km2 grid cells. A Bayesian state-space occupancy model was used to predict probability of suitable habitat from the field data.
3.The Maxent and occupancy models predicted similar spatial distributions of habitat suitability for sambar deer in Victoria and there was a strong positive correlation between the rankings of cells by the two approaches. The congruence of the two models suggests that any spatial and detection biases in the presence-only data were relatively unimportant in our study.
4.We predicted the extent of suitable habitat from the occupancy model using a threshold that gave a false negative error rate of 005. The current distribution was the suitable habitat within a kernel that had a 995% chance of including the presence locations pooled from incidental sightings and field surveys: the potential distribution was suitable habitat outside that kernel. Several discrete areas of potential distribution were identified as priorities for surveillance monitoring with the aim of detecting and managing incursions of sambar deer.
Secondly, we searched for signs of sambar deer along a 400 m transect in each of the 80 cells. The sign transect was subjectively located by field staff to maximize the detection of deer (e.g. along a trail or watercourse likely to be used by sambar deer; Bentley 1998). Any of the following signs of sambar deer seen along the survey route were recorded: sightings of live or dead deer, tree-rubbings, tracks, cast antlers, wallows and faecal pellets. The presence/absence of sambar deer sign on transects was denoted as Yi4 = 1 and 0, respectively. 041b061a72