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"Abysses."
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Viaje por el abismo: Kafka en la antipoesía de Nicanor Parra
The presence of Franz Kafka’s influence in various Latin American narrative writers is well known and studied. Less known is the influence Kafka had on the Chilean (anti)poet Nicanor Parra. Some of the most prominent critics of Parra’s work mention it, but it has not been studied in depth. This present article tries to shine light on the antiheroism, dark humor and the anxiety of mortality which are common for both Parra and Kafka.
Journal Article
Taxonomy and functional profile of microbial communities across the depths of the Alpine Cenote Abyss ice cave
Investigating the geomicrobiology of the cryosphere offers insights into past climate dynamics and the potential impacts of ongoing climate change. Here, we present the characterization of the microbial communities inhabiting ice sediments collected at various depths within the Cenote Abyss cave, located in the Italian Alps. First explored in 1994 following the drainage of an overlying lake, this site harbours one of the largest cave glaciers in the Dolomites. Metabarcoding and metagenomic analyses revealed a dominance of cold-adapted bacterial taxa, primarily Actinomycetota, Bacteroidota, and Pseudomonadota, with functional genes linked to distinct steps of the nitrogen cycle varying by cave depth. From the shallowest to the deepest ice cave zones, microbial communities shifted from nitrogen-fixing bacterial genera, including
Parafrigobacterium
,
Polaromonas
, and
Pedobacter
, to a higher prevalence of nitrifying bacteria such as
Nitrospira
. Functional metagenomic analyses revealed that genes involved in nitrogen and carbon cycling are broadly distributed across the cave depth zones, with the inner samples displaying the highest potential for nitrogen transformations, including complete denitrification pathways. CO₂ fixation pathways, including the Calvin–Benson–Bassham and Wood–Ljungdahl cycles, were partially represented and taxonomically diverse across the cave depths. Culturable bacterial strains from all depths demonstrated enzymatic activities relevant to organic matter degradation, while phenotype microarray analysis highlighted the metabolic versatility of the inner microbial community in utilizing organic nitrogen substrates, supporting the higher diversity of the inner cave zone compared to the outer cave zone. These findings underscore the ecological complexity and functional potential of microbial life in subterranean ice, offering insights into biogeochemical processes in cold and nutrient-poor environments with implications for climate change studies.
Journal Article
Confirmation of hard-substrate predictions in the abyssal Vema Fracture Zone
Hydroacoustic mapping has recently challenged the long-held view of a uniform abyssal seafloor by predicting substantial habitat heterogeneity in this environment. The RUBBLE expedition M205 validated these predictions in the Vema Fracture Zone (VFZ) with visual surveys at six locations using a towed deep-sea camera system. Exposed rock outcrops and varied hard substrates were consistently confirmed in areas of high hard-rock exposure, while moderately predicted areas contained a mix of sediments, cobbles, and pebbles; low-potential sites were almost entirely covered in sediment. Although a detailed quantification is beyond the scope of this report, visual correspondence supports the reliability of hydroacoustic predictions for abyssal habitats. Notably, this study pioneers the application of hydroacoustic-based seafloor characterization at abyssal depths—extending methods formerly focused on bathyal zones to the planet’s largest benthic environment and enabling direct ground-truthing of habitat models below 5,000 m. These findings highlight abyssal habitat heterogeneity, confirm the utility of hydroacoustic tools for broad-scale benthic mapping, and establish a baseline for future research on deep-sea biodiversity and ecological dynamics.
Journal Article
Application of the GIS methods along with measured parameters to identify the NH4+ origin in the Hranice Karst (Czech Republic)
The study aims to determine the source of NH4+ ions in the mineral waters of the Hranice Karst. The study area is located in the eastern part of the Czech Republic, Europe. The area is known mainly for its carbon dioxide of deep origin; the gas was the factor that enabled the formation of hypogene karst, in the Palaeozoic limestones, as well as warm mineral waters. The limestones of the area are covered by Neogene (Miocene) sediments of variable thickness and lithology. Recurrent sampling was done at 36 sites. A total of 96 surface water samples, 65 borehole water samples and 96 karst water samples were assessed. Major anions, cations and the content of nitrogen and its forms were determined for all water samples. The soil types were characterised by a field pedological survey. The normalised difference vegetation index was calculated in QGIS and vegetation vitality was evaluated. Since places with remarkably low vegetation index were found to be linked to the occurrence of Miocene sandstones, they represent points of rather fast entry of rainwater into the ground. As the presence of carbon dioxide creates an anoxic setting underground, the entering nitrates are transformed into NH4+ ions. This mechanism of transformation within the nitrogen cycle explains the presence of NH4+ ions in areas with elevated CO2.
Journal Article
On Black Poetry: The Corpse and the Phenomenon of Third-Person Consciousness
Blackness, simply, is not . Or, more aptly put— the naught-ness of not . Blackness exists in uncertain terms caught —petrified within meanings fashioned by the violent discourse of culture. Yet, Blackness insists on masquerading within those meanings, performing the transgressive and operating within its own abyssal effects that fundamentally “damage” the laws of discourse. Similarly functioning from a familiar position of theoretical negativity, poetry philosophically represents that which cannot fully arrive—“an affair of ‘private language.” What happens when Blackness encounters the private language of poetry? How does Blackness accomplish the work of utterance facing the impossibility of its being within the operations of the poetic and its silences? What is Black poetry? This paper surveys the convergence of Blackness with poetry, insisting that Blackness presents an aesthetic conundrum to the affairs of language. From this meeting between two negativities, the following questions emerge: What can Black poetry represent? What of naught-ness can be established in the realm of appearances? In this paper, I will argue that under the pressure of anti-Black discourse, Blackness pretends to be— performing itself as poetry. Consulting the theoretical work of David Marriott and Jean-François Lyotard, I will attempt to locate this performance in Melvin Dixon’s poetry collection Love’s Instruments .
Journal Article
An updated de novo transcriptome for green ash (Fraxinus pennsylvanica)
De novo transcriptome assembly of next-generation sequencing information has become a powerful tool for the study of non-model species. Transcriptomes generated by this method can have high variability due to endless combinations of user-defined variables and programs available for assembly. Many methods have been developed for evaluating the quality of these assemblies. Here, raw sequencing information for Green ash (Fraxinus pennsylvanica Marshall) that was previously published has been re-evaluated. An updated assembly has been developed by including additional sequencing information not used for the currently accepted transcriptome in combination with more stringent trimming parameters. Input reads were assembled with Trinity and Abyss assembly programs. The resulting Trinity assembly has a 7.3-fold increase in genomic breadth of coverage, a 2.4-fold increase in predicted complete open reading frames, an increased L50 value, and increased Benchmarking Universal Single-Copy Ortholog completeness compared to the earlier published transcriptome. This updated transcriptome can be leveraged to help fight the rapid decline of green ash due to pathogens.
Journal Article
Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes
Background
Alternative polyadenylation (APA) results in messenger RNA molecules with different 3′ untranslated regions (3’ UTRs), affecting the molecules’ stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3’ UTR length modifications and commonly characterized APA events as 3’ UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3′ ends of transcripts and fails to adequately describe the various scenarios we observe.
Results
We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT. We applied this pipeline to elucidate the APA profiles of 114 genes in 9939 tumor and 729 tissue normal samples from The Cancer Genome Atlas (TCGA). The full set of 10,668 RNA-Seq samples from 33 cancer types has not been utilized by previous APA studies. By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types; for 15 genes, such regulation is recurrent across multiple cancers. Our results also support a previous report showing the 3’ UTR shortening of
FGF2
in multiple cancers. However, over half of the events we identified display complex changes to 3’ UTR length that resist simple classification like shortening or lengthening.
Conclusions
Recurrent tumor-specific regulation of APA is widespread in cancer. However, the regulation pattern that we observed in TCGA RNA-seq data cannot be described as straightforward 3’ UTR shortening or lengthening. Continued investigation into this complex, nuanced regulatory landscape will provide further insight into its role in tumor formation and development.
Journal Article
Abyssal fauna of polymetallic nodule exploration areas, eastern Clarion-Clipperton Zone, central Pacific Ocean: Annelida: Spionidae and Poecilochaetidae
This paper represents a continuation of taxonomic publications on the benthic fauna of polymetallic nodule fields in the eastern ClarionClipperton Zone (CCZ) using material collected during baseline environmental survey work targeting two exploration contract areas (“UK-1” and “OMS”) and one Area of Particular Environmental Interest, “APEI-6.” Families Poecilochaetidae Hannerz, 1956 and Spionidae Grube, 1850 of the annelid suborder Spioniformia were studied here. Taxonomic data are presented for 25 species from 98 records as identified by a combination of morphological and genetic approaches. Although sub-optimal morphological condition can prevent new species being formally described, it is essential that morphological, molecular, and voucher data are made available for future surveys. Descriptions of two new species—Poecilochaetus brenkei sp.nov.andLaonice shulseae sp. nov.—increase the number of formally described new annelid species from the areas targeted in this study to 15 and CCZ-wide to 46. We also discuss the commonly reported “cosmopolitan” deep-sea spionid Aurospio dibranchiata Maciolek, 1981, which we show represents several genetically distinct species (three of these from CCZ area alone) but without reliable morphological characters to separate them. Molecular data provide evidence that 15 out of 25 species reported here have a wide distribution within the eastern CCZ and that Aurospio sp. “NHM_2186” and the known species Prionospio amarsupiata Neal & Altamira in Paterson et al. 2016 may be cosmopolitan. Lastly, the molecular data provide insights into relationships within Spioniformia, suggesting that both Poecilochaetidae and Trochochaetidae belong within Spionidae.
Journal Article