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1.
Mol Cell ; 76(6): 909-921.e3, 2019 12 19.
Article in English | MEDLINE | ID: mdl-31676231

ABSTRACT

Metabolic signaling to chromatin often underlies how adaptive transcriptional responses are controlled. While intermediary metabolites serve as co-factors for histone-modifying enzymes during metabolic flux, how these modifications contribute to transcriptional responses is poorly understood. Here, we utilize the highly synchronized yeast metabolic cycle (YMC) and find that fatty acid ß-oxidation genes are periodically expressed coincident with the ß-oxidation byproduct histone crotonylation. Specifically, we found that H3K9 crotonylation peaks when H3K9 acetylation declines and energy resources become limited. During this metabolic state, pro-growth gene expression is dampened; however, mutation of the Taf14 YEATS domain, a H3K9 crotonylation reader, results in de-repression of these genes. Conversely, exogenous addition of crotonic acid results in increased histone crotonylation, constitutive repression of pro-growth genes, and disrupted YMC oscillations. Together, our findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.


Subject(s)
Acyl Coenzyme A/metabolism , Energy Metabolism , Gene Expression Regulation, Fungal , Histones/metabolism , Protein Processing, Post-Translational , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Transcription Factor TFIID/metabolism , Energy Metabolism/genetics , Fatty Acids/metabolism , Histones/genetics , Homeostasis , Lysine , Oxidation-Reduction , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Signal Transduction , Transcription Factor TFIID/genetics , Transcription, Genetic
2.
Nature ; 586(7827): 70-74, 2020 10.
Article in English | MEDLINE | ID: mdl-32999481

ABSTRACT

The Greenland Ice Sheet (GIS) is losing mass at a high rate1. Given the short-term nature of the observational record, it is difficult to assess the historical importance of this mass-loss trend. Unlike records of greenhouse gas concentrations and global temperature, in which observations have been merged with palaeoclimate datasets, there are no comparably long records for rates of GIS mass change. Here we reveal unprecedented mass loss from the GIS this century, by placing contemporary and future rates of GIS mass loss within the context of the natural variability over the past 12,000 years. We force a high-resolution ice-sheet model with an ensemble of climate histories constrained by ice-core data2. Our simulation domain covers southwestern Greenland, the mass change of which is dominated by surface mass balance. The results agree favourably with an independent chronology of the history of the GIS margin3,4. The largest pre-industrial rates of mass loss (up to 6,000 billion tonnes per century) occurred in the early Holocene, and were similar to the contemporary (AD 2000-2018) rate of around 6,100 billion tonnes per century5. Simulations of future mass loss from southwestern GIS, based on Representative Concentration Pathway (RCP) scenarios corresponding to low (RCP2.6) and high (RCP8.5) greenhouse gas concentration trajectories6, predict mass loss of between 8,800 and 35,900 billion tonnes over the twenty-first century. These rates of GIS mass loss exceed the maximum rates over the past 12,000 years. Because rates of mass loss from the southwestern GIS scale linearly5 with the GIS as a whole, our results indicate, with high confidence, that the rate of mass loss from the GIS will exceed Holocene rates this century.

3.
Nature ; 572(7770): 461-466, 2019 08.
Article in English | MEDLINE | ID: mdl-31340216

ABSTRACT

Effective ocean management and the conservation of highly migratory species depend on resolving the overlap between animal movements and distributions, and fishing effort. However, this information is lacking at a global scale. Here we show, using a big-data approach that combines satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space-use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively), and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of fishing effort in marine areas beyond national jurisdictions (the high seas). Our results demonstrate an urgent need for conservation and management measures at high-seas hotspots of shark space use, and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real-time, dynamic management.


Subject(s)
Animal Migration , Fisheries/statistics & numerical data , Geographic Mapping , Oceans and Seas , Sharks/physiology , Spatio-Temporal Analysis , Animals , Population Density , Risk Assessment , Sharks/classification , Ships , Time Factors
4.
Proc Natl Acad Sci U S A ; 119(36): e2116841119, 2022 09 06.
Article in English | MEDLINE | ID: mdl-36037379

ABSTRACT

Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane- and cell-wall-associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.


Subject(s)
Fungi , Life Cycle Stages , Phylogeny , Diploidy , Fungi/classification , Fungi/genetics , Genome, Fungal/genetics
5.
Proc Natl Acad Sci U S A ; 119(7)2022 02 15.
Article in English | MEDLINE | ID: mdl-35131944

ABSTRACT

The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.


Subject(s)
Air Microbiology , Bacteria/classification , Bacteria/isolation & purification , Aerosols , Altitude , Atmosphere , Humans
6.
Proc Natl Acad Sci U S A ; 119(20): e2117440119, 2022 05 17.
Article in English | MEDLINE | ID: mdl-35533277

ABSTRACT

Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks' horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial "cryptic" lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.


Subject(s)
Sharks , Animals , Endangered Species , Plankton , Ships
7.
Plant J ; 115(5): 1214-1230, 2023 09.
Article in English | MEDLINE | ID: mdl-37219088

ABSTRACT

Identification of protein interactors is ideally suited for the functional characterization of small molecules. 3',5'-cAMP is an evolutionary ancient signaling metabolite largely uncharacterized in plants. To tap into the physiological roles of 3',5'-cAMP, we used a chemo-proteomics approach, thermal proteome profiling (TPP), for the unbiased identification of 3',5'-cAMP protein targets. TPP measures shifts in the protein thermal stability upon ligand binding. Comprehensive proteomics analysis yielded a list of 51 proteins significantly altered in their thermal stability upon incubation with 3',5'-cAMP. The list contained metabolic enzymes, ribosomal subunits, translation initiation factors, and proteins associated with the regulation of plant growth such as CELL DIVISION CYCLE 48. To functionally validate obtained results, we focused on the role of 3',5'-cAMP in regulating the actin cytoskeleton suggested by the presence of actin among the 51 identified proteins. 3',5'-cAMP supplementation affected actin organization by inducing actin-bundling. Consistent with these results, the increase in 3',5'-cAMP levels, obtained either by feeding or by chemical modulation of 3',5'-cAMP metabolism, was sufficient to partially rescue the short hypocotyl phenotype of the actin2 actin7 mutant, severely compromised in actin level. The observed rescue was specific to 3',5'-cAMP, as demonstrated using a positional isomer 2',3'-cAMP, and true for the nanomolar 3',5'-cAMP concentrations reported for plant cells. In vitro characterization of the 3',5'-cAMP-actin pairing argues against a direct interaction between actin and 3',5'-cAMP. Alternative mechanisms by which 3',5'-cAMP would affect actin dynamics, such as by interfering with calcium signaling, are discussed. In summary, our work provides a specific resource, 3',5'-cAMP interactome, as well as functional insight into 3',5'-cAMP-mediated regulation in plants.


Subject(s)
Actin Cytoskeleton , Actins , Actins/metabolism , Actin Cytoskeleton/metabolism , Plants/metabolism , Calcium Signaling
8.
J Am Chem Soc ; 146(14): 9728-9740, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38535624

ABSTRACT

A lack of suitable high-potential catholytes hinders the development of aqueous redox flow batteries (RFBs) for large-scale energy storage. Hydrolysis of the charged (oxidized) catholyte typically occurs when its redox potential approaches that of water, with a negative impact on battery performance. Here, we elucidate and address such behavior for a representative iron-based organometallic complex, showing that the associated voltage and capacity losses can be curtailed by several simple means. We discovered that addition of activated carbon cloth (ACC) to the reservoir of low-cost, high-potential [Fe(bpy)3]2+/3+ catholyte-limited aqueous redox flow batteries extends their lifetime and boosts discharge voltage─two typically orthogonal performance metrics. Similar effects are observed when the catholyte's graphite felt electrode is electrochemically oxidized (overcharged) and by modifying the catholyte solution's pH, which was monitored in situ for all flow batteries. Modulation of solution pH alters hydrolytic speciation of the charged catholyte from the typical dimeric species µ-O-[FeIII(bpy)2(H2O)]24+, converting it to a higher-potential µ-dihydroxo form, µ-[FeIII(bpy)2(H2O)(OH)]24+, at lower pH. The existence of free bpyH22+ at low pH is found to strongly correlate with battery degradation. Near-neutral-pH RFBs employing a viologen anolyte, (SPr)2V, in excess with the [Fe(bpy)3]2+/3+ catholyte containing ACC exhibited high-voltage discharge for up to 600 cycles (41 days) with no discernible capacity fade. Correlating pH and voltage data offers powerful fundamental insight into organometallic (electro)chemistry with potential utility beyond battery applications. The findings, with implications toward a host of other "near-neutral" active species, illuminate the critical and underappreciated role of electrolyte pH on intracycle and long-term aqueous flow battery performance.

9.
Genome Res ; 31(7): 1216-1229, 2021 Jul.
Article in English | MEDLINE | ID: mdl-33975875

ABSTRACT

Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e., paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are coexpressed in the cell and thus can compete for target sites across the genome. However, this competition is rarely taken into account when studying the in vivo binding patterns of eukaryotic TFs. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data show that Cbf1 and Pho4 greatly influence each other's occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs' expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.

10.
PLoS Biol ; 19(8): e3001108, 2021 08.
Article in English | MEDLINE | ID: mdl-34375335

ABSTRACT

Sharks (Selachimorpha) are iconic marine predators that have survived multiple mass extinctions over geologic time. Their prolific fossil record is represented mainly by isolated shed teeth, which provide the basis for reconstructing deep time diversity changes affecting different selachimorph clades. By contrast, corresponding shifts in shark ecology, as measured through morphological disparity, have received comparatively limited analytical attention. Here, we use a geometric morphometric approach to comprehensively examine tooth morphologies in multiple shark lineages traversing the catastrophic end-Cretaceous mass extinction-this event terminated the Mesozoic Era 66 million years ago. Our results show that selachimorphs maintained virtually static levels of dental disparity in most of their constituent clades across the Cretaceous-Paleogene interval. Nevertheless, selective extinctions did impact apex predator species characterized by triangular blade-like teeth. This is particularly evident among lamniforms, which included the dominant Cretaceous anacoracids. Conversely, other groups, such as carcharhiniforms and orectolobiforms, experienced disparity modifications, while heterodontiforms, hexanchiforms, squaliforms, squatiniforms, and †synechodontiforms were not overtly affected. Finally, while some lamniform lineages disappeared, others underwent postextinction disparity increases, especially odontaspidids, which are typified by narrow-cusped teeth adapted for feeding on fishes. Notably, this increase coincides with the early Paleogene radiation of teleosts as a possible prey source, and the geographic relocation of disparity sampling "hotspots," perhaps indicating a regionally disjunct extinction recovery. Ultimately, our study reveals a complex morphological response to the end-Cretaceous mass extinction and highlights an event that influenced the evolution of modern sharks.


Subject(s)
Biological Evolution , Extinction, Biological , Fossils/anatomy & histology , Sharks/anatomy & histology , Tooth/anatomy & histology , Animals , Ecosystem
11.
Clin Anat ; 37(3): 337-343, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38251059

ABSTRACT

Almost 20% of the Latin nouns (193/993) in Terminologia Histologica (TH), the international standard nomenclature for human histology and cytology, display linguistic problems, particularly in the areas of orthography, gender, and declension. Some anatomists have opposed efforts to restore the quality of the Latin nomenclature as pedantry, preferring to create or modify Latin words so that they resemble words in English and other modern languages. A Latin microanatomical nomenclature is vulnerable to the criticism of anachronism, so the requirement for the use of authentic Latin, including derivation of new words from Greek and Latin words rather than from modern languages, if possible, may be even greater than it is for the anatomical nomenclature. The most common problem identified here appears to have been caused by derivation of Latin nouns by addition of -us and -um second declension endings to English words. Many Latin nouns (128) in TH contain one of six morphemes that have been treated this way even though the original Greek words are either first declension masculine or third declension neuter nouns. Ironically, deriving Latin nouns directly from Greek morphemes often results in words that look more familiar to speakers of Romance and Germanic languages than those derived indirectly through modern languages (e.g., astrocyte, collagene, dendrita, lipochroma, osteoclasta and telomere instead of astrocytus, collagenum, dendritum, lipochromum, osteoclastus, and telomerus).


Subject(s)
Anatomists , Vocabulary , Humans , Language , Linguistics
12.
Clin Anat ; 2024 Sep 08.
Article in English | MEDLINE | ID: mdl-39245875

ABSTRACT

In medical education, traditional anatomy labs have relied heavily on the hands-on dissection of cadavers to teach the complex spatial relationships within the human body. However, the advent of virtual reality (VR) technology offers the potential for significantly enhancing this traditional approach by providing immersive, interactive 3D visualizations that can overcome some of the limitations of physical specimens. This study explores the integration of VR into a traditional gross anatomy lab to enrich the learning experience for medical students. Methods included the deployment of a VR application developed to complement the dissection process, featuring detailed 3D models of human anatomy that students could manipulate and explore digitally. Approximately 60 s-year medical students participated in the lab, where they engaged with both traditional dissection and the VR application. Results indicated that the VR integration not only increased engagement and satisfaction but also improved the students' ability to understand anatomical structures and their spatial relationships. Moreover, feedback from students suggested more efficient learning and retention than with traditional methods alone. We conclude that VR technology can significantly enhance medical anatomy education by providing an adjunct to traditional dissection, potentially replacing certain aspects of physical specimens with digital simulations that offer repeatable, detailed exploration without the associated logistical and ethical constraints.

13.
Clin Anat ; 37(1): 12-24, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37453079

ABSTRACT

Gamification has appeared as an alternative educational methodology to traditional tools. Specifically, in anatomy teaching, multiple technological applications have emerged in response to the difficulties of accessing cadaveric material; however, there is insufficient information about the effects of these applications on the performance achieved by students, or about to the best way to adapt learning to meet their educational needs. In this study, we investigated how teaching human anatomy through a mobile gamified technological tool containing recommendation systems can be combined with a virtual assistant to improve the learning and academic performance of medical students in the Anatomy Department at the Universidad de La Frontera in Temuco, Chile and the Anatomy Department at the Pontificia Universidad Católica de Chile. In total, 131 students participated in the experiment, which was divided into two case studies. The main findings led to the conclusion that gamified components support students in learning anatomy. In addition, the predictions and recommendations provided by the virtual assistant enabled the academic aspects that the students needed to improve to be extracted adequately. Future work is expected to support adaptive learning by incorporating new artificial intelligence in education elements that can generate personalized scenarios for studying anatomy based on the application.


Subject(s)
Anatomy , Education, Medical , Humans , Gamification , Artificial Intelligence , Learning , Power, Psychological , Anatomy/education
14.
Nano Lett ; 23(4): 1467-1473, 2023 Feb 22.
Article in English | MEDLINE | ID: mdl-36753635

ABSTRACT

We report spin-polarized transient absorption for colloidal CdSe nanoplatelets as functions of thickness (2-6 monolayer thickness) and core/shell motif. Using electro-optical modulation of co- and cross-polarization pump-probe combinations, we sensitively observe spin-polarized transitions. Core-only nanoplatelets exhibit few-picosecond spin lifetimes that weakly increase with layer thickness. The spectral content of differenced spin-polarized signals indicate biexciton binding energies that decrease with increasing thickness and smaller values than previously reported. Shell growth of CdS with controlled thicknesses, which partially delocalize the electron from the hole, significantly increases the spin lifetime to ∼49 ps at room temperature. Implementation of ZnS shells, which do not alter delocalization but do alter surface termination, increased spin lifetimes up to ∼100 ps, bolstering the interpretation that surface termination heavily influences spin coherence, likely due to passivation of dangling bonds. Spin precession in magnetic fields both confirms long coherence lifetime at room temperature and yields the excitonic g factor.

15.
J Fish Biol ; 105(2): 482-511, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38852616

ABSTRACT

Levels of dissolved oxygen in open ocean and coastal waters are decreasing (ocean deoxygenation), with poorly understood effects on marine megafauna. All of the more than 1000 species of elasmobranchs (sharks, skates, and rays) are obligate water breathers, with a variety of life-history strategies and oxygen requirements. This review demonstrates that although many elasmobranchs typically avoid hypoxic water, they also appear capable of withstanding mild to moderate hypoxia with changes in activity, ventilatory responses, alterations to circulatory and hematological parameters, and morphological alterations to gill structures. However, such strategies may be insufficient to withstand severe, progressive, or prolonged hypoxia or anoxia where anaerobic metabolic pathways may be used for limited periods. As water temperatures increase with climate warming, ectothermic elasmobranchs will exhibit elevated metabolic rates and are likely to be less able to tolerate the effects of even mild hypoxia associated with deoxygenation. As a result, sustained hypoxic conditions in warmer coastal or surface-pelagic waters are likely to lead to shifts in elasmobranch distributions. Mass mortalities of elasmobranchs linked directly to deoxygenation have only rarely been observed but are likely underreported. One key concern is how reductions in habitat volume as a result of expanding hypoxia resulting from deoxygenation will influence interactions between elasmobranchs and industrial fisheries. Catch per unit of effort of threatened pelagic sharks by longline fisheries, for instance, has been shown to be higher above oxygen minimum zones compared to adjacent, normoxic regions, and attributed to vertical habitat compression of sharks overlapping with increased fishing effort. How a compound stressor such as marine heatwaves alters vulnerability to deoxygenation remains an open question. With over a third of elasmobranch species listed as endangered, a priority for conservation and management now lies in understanding and mitigating ocean deoxygenation effects in addition to population declines already occurring from overfishing.


Subject(s)
Oxygen , Sharks , Animals , Oxygen/metabolism , Sharks/physiology , Skates, Fish/physiology , Oceans and Seas , Elasmobranchii/physiology , Climate Change
16.
Proteins ; 91(10): 1394-1406, 2023 10.
Article in English | MEDLINE | ID: mdl-37213073

ABSTRACT

Chemotaxis is a fundamental process whereby bacteria seek out nutrient sources and avoid harmful chemicals. For the symbiotic soil bacterium Sinorhizobium meliloti, the chemotaxis system also plays an essential role in the interaction with its legume host. The chemotactic signaling cascade is initiated through interactions of an attractant or repellent compound with chemoreceptors or methyl-accepting chemotaxis proteins (MCPs). S. meliloti possesses eight chemoreceptors to mediate chemotaxis. Six of these receptors are transmembrane proteins with periplasmic ligand-binding domains (LBDs). The specific functions of McpW and McpZ are still unknown. Here, we report the crystal structure of the periplasmic domain of McpZ (McpZPD) at 2.7 Å resolution. McpZPD assumes a novel fold consisting of three concatenated four-helix bundle modules. Through phylogenetic analyses, we discovered that this helical tri-modular domain fold arose within the Rhizobiaceae family and is still evolving rapidly. The structure, offering a rare view of a ligand-free dimeric MCP-LBD, reveals a novel dimerization interface. Molecular dynamics calculations suggest ligand binding will induce conformational changes that result in large horizontal helix movements within the membrane-proximal domains of the McpZPD dimer that are accompanied by a 5 Å vertical shift of the terminal helix toward the inner cell membrane. These results suggest a mechanism of transmembrane signaling for this family of MCPs that entails both piston-type and scissoring movements. The predicted movements terminate in a conformation that closely mirrors those observed in related ligand-bound MCP-LBDs.


Subject(s)
Bacterial Proteins , Sinorhizobium meliloti , Bacterial Proteins/chemistry , Sinorhizobium meliloti/genetics , Sinorhizobium meliloti/metabolism , Phylogeny , Methyl-Accepting Chemotaxis Proteins/chemistry , Methyl-Accepting Chemotaxis Proteins/genetics , Methyl-Accepting Chemotaxis Proteins/metabolism , Chemotaxis/physiology
17.
PLoS Comput Biol ; 18(6): e1009846, 2022 06.
Article in English | MEDLINE | ID: mdl-35696439

ABSTRACT

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNet's capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin α4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains.


Subject(s)
Image Processing, Computer-Assisted , Neural Stem Cells , Image Processing, Computer-Assisted/methods , Neurons , Spatio-Temporal Analysis
18.
An Acad Bras Cienc ; 95(2): e20201519, 2023.
Article in English | MEDLINE | ID: mdl-37075371

ABSTRACT

Sexual dimorphism has often been recorded in apple snails (Caenogastropoda Ampullariidae), but reports are concentrated in a few species, either invasive or with biocontrol potential, which sugests some taxonomic bias. To find out evolutionary and ecological correlates of sexual dimorphism it is necessary to detect and quantify it but also is important to detect its absence. Our aims were to confirm or not the existence of sexual dimorphism in shell shape of Felipponea neritiniformis and Asolene platae, using Pomacea canaliculata as reference and applying the same methodology (landmark-based geometric morphometrics) and statistical power. Significant intersexual differences were only found in P. canaliculata and, in a lesser degree, in F. neritiniformis: males have larger apertures relative to body whorl and more rounded apertural outer edges than females. Female shells are larger in F. neritiniformis and P. canaliculata, but not in A. platae. Using comparable methodologies and statistical power, sexual dimorphism in shell shape is detectable in some apple snails but not in others. Interspecific variation in sexual dimorphism in the Ampullariidae is not only due to taxonomic bias and deserves more research to establish the main patterns and possible causes.


Subject(s)
Sex Characteristics , Snails , Animals , Male , Female , Phylogeny , Biological Evolution
19.
An Acad Bras Cienc ; 95(2): e20210516, 2023.
Article in English | MEDLINE | ID: mdl-37075376

ABSTRACT

Melanoides tuberculata is a freshwater snail native to Old World tropical areas but has invaded tropical and subtropical regions around the world. In Argentina, populations established in natural environments were reported from northeastern tropical provinces. Here we report for the first time the presence of M. tuberculata in a geothermally warmed channel in temperate Southern Pampas. We mapped its distribution in the channel, searched for its presence in five nearby basins, estimated the risk of establishment and expansion in Argentina with distribution models and analyzed shape variation through geometric morphometrics. Melanoides tuberculata was recorded exclusively in the channel in sites with temperatures between 20 and 40°C, with almost no overlap with other snails. No evidence of M. tuberculata was found in nearby basins. The distribution model predicted that only northernmost areas from Argentina are suitable for this species, where it could impact snail communities and food webs if introduction through the aquarium trade is not prevented. The absence of males indicates parthenogenetic reproduction and probably a recent invasion. Shell shape variation in this population, 15 % of which is attributable to allometry, encompasses the shapes of specimens from other South American populations, suggesting that all belong to the same lineage.


Subject(s)
Lepidoptera , Snails , Animals , Male , Fresh Water , Food Chain , Argentina
20.
Clin Anat ; 36(5): 708-714, 2023 Jul.
Article in English | MEDLINE | ID: mdl-36752958

ABSTRACT

Previous studies have not verified the contents of accessory foramina of the zygomatic bone on dry skulls and thus could not conclude whether they carried accessory zygomaticofacial nerve branches or branches or the entire trunk of the zygomaticotemporal nerve (ZTN). Therefore, the aim of the current study is to present findings from cadaveric dissections to clarify this relationship. Fifty, fresh frozen, adult cadaveric sides underwent dissection of the ZTN. When identified, these nerves were quantified and their relationship to the zygomatic bone further documented by dissecting through the bone following the course of the nerve from a superficial to deep perspective. Additionally, 100 dry, adult, human skulls were analyzed looking for lateral foramina on the zygomatic bone. On three cadaveric sides (6%), the ZTN was found to pierce the zygomatic bone deeply and exit its superficial lateral surface. For dry skull specimens, a lateral zygomaticotemporal foramen (ZTF) was identified on nine sides (4.5%). For both groups, the presence of a strong marginal process of the zygomatic bone was strongly correlated to a ZTF exiting the lateral surface of the zygomatic bone. Although relatively uncommon, the ZTN can pierce the lateral aspect of the zygomatic bone and thus can be located superficial to the cheek. Such findings should be borne in mind during surgical or other invasive procedures in this area in order to minimize iatrogenic injury to the ZTN.


Subject(s)
Skull , Zygoma , Adult , Humans , Zygoma/anatomy & histology , Face , Cheek , Cadaver
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