Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

Proximal and distal transformation during intercalary regeneration in the planarianDugesia(S)mediterranea

Summary Studies on intercalary regeneration in several organisms have shown that a regenerate is formed when surfaces of different positional value along the proximo-distal axis are opposed. One of the main problems posed by this phenomenon is to know which piece contributes to the building of the regenerate. In the present work we have studied this problem in planarians using chimaeras made between pieces of different body levels, irradiated or not, of the sexual and asexual races ofDugesia(S)mediterranea that differ in a chromosomal marker.The results found show very clearly that intercalary regenerates in planarians are formed by cells coming from both pieces (stumps), and that irradiated pieces keep the positional values and interact with non-irradiated pieces to restore the missing parts. This means that distal and proximal transformation do actually occur at the same time during intercalary regeneration in planarians. The implications of these results as regards to the origin of cells in the regenerate and to present models of intercalary regeneration are discussed.     

Factors Determining Annual Changes in Bacterial Photosynthetic Pigments in Holomictic Lake Cisó, Spain

The pigments and biomass of anoxygenic phototrophic bacteria were measured during a year cycle in Lake Cisó (Girona, Spain). Two genera, Chromatium and Chlorobium, accounted for most of the bacterial population. The bacteria were present throughout the year despite complete mixing of the lake during fall and winter. This was possible because the sulfide production in the sediment was high enough to make the lake anaerobic to the very surface. Solar radiation, temperature, and biomass of Chromatium sp. were found to be important in determining pigment concentrations by correlation analysis. Sulfide concentration and biomass of Chlorobium spp. were found to be unimportant. A path analysis was performed to determine what percentage of the variability of pigments could be explained by the variables studied. Since a high percentage could be explained, it was possible to conclude that solar radiation, temperature, and biomass of Chromatium sp. were the main variables.     

Lindane Administration to the Rat Induces Modifications in the Regional Cerebral Binding of [3H]Muscimol, [3H]-Flunitrazepam, and t-[35S]Butylbicyclophosphorothionate: An Autoradiographic Study

Abstract: The effect of lindane administration on the specific binding of ligands to different sites on the GABA_A receptor-ionophore complex was studied in the rat brain by receptor mapping autoradiography. [³H]Muscimol (Mus), [³H]flunitrazepam (Flu), and t -[³⁵S]butylbicyclophosphorothionate (TBPS) were used as specific ligands of GABA, benzodiazepine, and picrotoxinin binding sites, respectively. Rats received a single oral dose of 30 mg/kg lindane and they were classified into two groups according to the absence or presence of convulsions. Vehicle-treated groups acted as controls. The effect of the xenobiotic on ligand binding was measured in different brain areas and nuclei 12 min or 5 h after its administration. Lindane induced a generalized decrease in [³⁵S]TBPS binding, which was present shortly after dosing. In addition, [³H]Flu binding was increased in lindane-treated animals, this modification also appearing shortly after administration but diminishing during the studied time. Finally, lindane induced a decrease in [³H]Mus binding, which became more evident over time. These modifications were observed both in the presence and in the absence of convulsions. However, an increase in [³H]-Mus binding was detected shortly after lindane-induced convulsions. The observed decrease in [³⁵S]TBPS binding is in agreement with the postulated action of lindane at the picrotoxinin binding site of the GABA_A receptor chloride channel. The effects observed on the binding of [³H]Flu and [³H]Mus may be secondary to the action of lindane as an allosteric antagonist of the GABA_A receptor.     

Two centuries of spatial and temporal dynamics of freshwater fish introductions

Aim

Investigating major freshwater fish flows (translocations) between biogeographic regions and their temporal dynamics and also quantifying spatial patterns and temporal changes in the array of introduced species, and the emergence and distance between major donor and recipient regions.

Location

Global.

Time Period

1800–2020.

Major Taxa Studied

Freshwater fishes.

Methods

We analysed a global dataset on freshwater fish introductions (4241 events of 688 species). Freshwater fish flows were investigated with flow diagrams and χ² tests, while PERMANOVA (permutational multivariate analysis of variance) was used to test the association between species and regions and temporal shifts. Cluster analysis revealed major recipient areas and composition of the introduced species. Finally, changes in distances between donor and recipient sites were tested with PERMANOVA.

Results

The number of introductions between biogeographic regions mirrored the European and North American dominance before World War II (WWII) and the trends in recreational fishing, biocontrol programmes and food production, especially in the Sino-Oriental region, which has a long tradition of aquaculture and fishkeeping. Over the years, the origins and composition of introduced species changed uniquely in each biogeographic region, although the most introduced species are common to every region. Salmonids and other cold-water species were frequently introduced before the 1950s, whereas tropical ornamental and aquaculture species currently prevail. Distances between donor and recipient sites did not vary over the time. After WWII, the Sino-Oriental region consolidated its dominance and the Ethiopian and Neotropical regions emerged as new global donor and recipient regions.

Main Conclusions

Global policy should focus on tropical ornamental and aquaculture species, which could benefit from global warming, especially in the Sino-Oriental region, because it currently dominates freshwater fish species flows, and the Ethiopian and Neotropical regions, because they recently emerged as important global donor and recipient regions of freshwater fish introductions.     

The freshwater planarian Dugesia (G.) tigrina contains a great diversity of homeobox genes

To identify potential pattern control and cell determination and/or differentiation genes in the freshwater planarian Dugesial (G.) tigrina, we searched for homeobox genes of different types in the genome of this primitive metazoan. We applied two basic approaches: 1) Screening the cDNA library with degenerate oligonucleotides corresponding to the most conserved amino acid sequence from helix-3 of the homeodomain of each family; and 2) PCR amplification of genomic DNA or cDNA, using two sets of degenerated oligonucleotides corresponding to helices 1 and 3 of the homeodomain or two specific domains of the POU family. Using the first strategy we have identified and characterized two tissue-specific cell determination and/or differentiation NK-type homeobox genes. Using the second strategy we have identified several homeobox genes that belong to the HOM/Hox, paired (prd) or POU families.     

Hypothesis: the target cell of GM-CSF is a macrophage precursor capable to produce cells with the property to secrete a G-CSF like activity.

The induction of granulocyte and macrophage colony formation by the granulocyte-macrophage colony stimulating factor (GM-CSF) on bone marrow cells (BMC) was evaluated as a function of time in agar cultures. We found that while macrophage cell clusters were very abundant on the first two days of culture, granulocytic cell clusters did not appear until the third day. We also found that macrophage colonies were present from the fourth day of culture, while granulocyte colonies did not appear until the fifth day. When two day cell clusters were transferred to cultures with GM-CSF we observed that only macrophage-colonies developed. On the other hand, when four day clusters were transferred, both granulocyte and macrophage colony formation was obtained in a similar way as the one obtained when using GM-CSF with fresh BMC. Two day clusters did not respond to granulocyte colony stimulating factor (G-CSF) while fourth day clusters generated granulocytic colonies in a similar way as when G-CSF was used with fresh BMC. In order to test the hypothesis that granulocyte colony formation in these assays could be a result of the secretion of G-CSF by the macrophages previously induced by GM-CSF, lysates from macrophage colonies were used to induce colony formation on BMC. We observed that colonies, mainly granulocytic, were induced in a similar way as when G-CSF was used. Finally, the possibility that GM-CSF is just a macrophage inducer with the property to produce cells that secrete G-CSF is discussed.     

Population dynamics ofTelenomus fariai [Hym.: Scelionidae], a parasite of chagas' disease vectors VIII. Morphological and ecological comparison between two allopatric populations under laboratory conditions

Telenomus fariai Lima ranges from Argentina and Chile to Mexico; some ecological parameters and morphological characters were compared between tropical (Costa Rica) and temperate (Argentina) populations, as reared on tropical and temperate hosts. The results of the 4 combinations between the 2 parasite populations and the 2 host species (Triatoma phyllosoma pallidipennis Stal) andTriatoma infestans Klug) [Hym.: Reduviidae] showed that only the parasite's geographical origin was statistically significant when evaluated through adult female life expectancy at time of emergence from the host, development time, total progeny per host per female 0–24 h old, and generation time. No difference was found between parasite populations with respect to total progeny per female and net reproductive rate. The morphometry proved statistically significant for all body measurements except the antennae.