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1.
Photosynth Res ; 157(2-3): 147-157, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37140874

RESUMO

We present here the life and the work of Paul A. Castelfranco (1921-2021), a very special person who was not only a top chemist of chlorophyll biosynthesis, but also made major contributions on fatty acid oxidation, acetate metabolism and cellular organization. He led an extraordinary and exemplary life as a human being. We present here both his personal life as well as his scientific life, which is followed by reminiscences by William Breidenbach, Kevin Smith, Alan Stemler, Ann Castelfranco, and John Castelfranco. As the subtitle of this Tribute implies, till the end Paul was a scientist par excellence, an intellectual with unlimited curiosity, a humanist, and a man of enduring religious faith. We all miss him dearly.

2.
Sci Data ; 10(1): 242, 2023 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-37105953

RESUMO

This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. 'Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study's primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.


Assuntos
Copépodes , Transcriptoma , Animais , Humanos , Sequência de Bases , Copépodes/genética
3.
Mol Ecol ; 31(6): 1753-1765, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35048451

RESUMO

How individual organisms adapt to nonoptimal conditions through physiological acclimatization is central to predicting the consequences of unusual abiotic and biotic conditions such as those produced by marine heat waves. The Northeast Pacific, including the Gulf of Alaska, experienced an extreme warming event (2014-2016, "The Blob") that affected all trophic levels and led to large-scale changes in the community. The marine copepod Neocalanus flemingeri is a key member of the subarctic Pacific pelagic ecosystem. During the spring phytoplankton bloom this copepod builds substantial lipid stores as it prepares for its nonfeeding adult phase. A 3-year comparison of gene expression profiles of copepods collected in Prince William Sound in the Gulf of Alaska between 2015 and 2017 included two high-temperature years (2015 and 2016) and one year with very low phytoplankton abundances (2016). The largest differences in gene expression were between high and low chlorophyll years, and not between warm and cool years. The observed gene expression patterns were indicative of physiological acclimatization. The predominant signal in 2016 was the down-regulation of genes involved in glycolysis and its incoming pathways, consistent with the modulation of metabolic rates in response to prolonged low food conditions. Despite the down-regulation of genes involved in metabolism, there was no evidence of suppression of protein synthesis based on gene expression or behavioural activity. Genes involved in muscle function were up-regulated, and the copepods were actively swimming and responsive to stimuli at collection. However, genes involved in fatty acid metabolism were down-regulated in 2016, suggesting reduced lipid accumulation.


Assuntos
Copépodes , Zooplâncton , Aclimatação/genética , Animais , Copépodes/genética , Ecossistema , Fitoplâncton , Zooplâncton/genética
5.
BMC Genomics ; 22(1): 409, 2021 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-34082716

RESUMO

BACKGROUND: Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development and metabolic suppression returning the organism to an active state. The physiological mechanisms that regulate the transition from diapause to post-diapause are still unknown. In this study, this transition has been characterized for the sub-arctic calanoid copepod Neocalanus flemingeri, a key crustacean zooplankter that supports the highly productive North Pacific fisheries. Transcriptional profiling of females, determined over a two-week time series starting with diapausing females collected from > 400 m depth, characterized the molecular mechanisms that regulate the post-diapause trajectory. RESULTS: A complex set of transitions in relative gene expression defined the transcriptomic changes from diapause to post-diapause. Despite low temperatures (5-6 °C), the switch from a "diapause" to a "post-diapause" transcriptional profile occurred within 12 h of the termination stimulus. Transcriptional changes signaling the end of diapause were activated within one-hour post collection and included the up-regulation of genes involved in the 20E cascade pathway, the TCA cycle and RNA metabolism in combination with the down-regulation of genes associated with chromatin silencing. By 12 h, females exhibited a post-diapause phenotype characterized by the up-regulation of genes involved in cell division, cell differentiation and multiple developmental processes. By seven days post collection, the reproductive program was fully activated as indicated by up-regulation of genes involved in oogenesis and energy metabolism, processes that were enriched among the differentially expressed genes. CONCLUSIONS: The analysis revealed a finely structured, precisely orchestrated sequence of transcriptional changes that led to rapid changes in the activation of biological processes paving the way to the successful completion of the reproductive program. Our findings lead to new hypotheses related to potentially universal mechanisms that terminate diapause before an organism can resume its developmental program.


Assuntos
Copépodes , Diapausa , Animais , Regiões Árticas , Copépodes/genética , Diapausa/genética , Feminino , Reprodução/genética , Transcriptoma
6.
Commun Biol ; 4(1): 426, 2021 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-33782539

RESUMO

Many arthropods undergo a seasonal dormancy termed "diapause" to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses to identify program-specific genes and biological processes. These analyses elucidated physiological differences and established protocols that distinguish between programs. Differences in gene expression were associated with maturation of individuals on the reproductive program, while those on the diapause program showed little change over time. Only two of six filters effectively separated copepods by developmental program. The first one included all genes annotated to RNA metabolism and this was confirmed using differential gene expression analysis. The second filter identified 54 differentially expressed genes that were consistently up-regulated in individuals on the diapause program in comparison with those on the reproductive program. Annotated to oogenesis, RNA metabolism and fatty acid biosynthesis, these genes are both indicators for diapause preparation and good candidates for functional studies.


Assuntos
Copépodes/fisiologia , Diapausa/genética , Transcriptoma/fisiologia , Animais , Copépodes/genética , Fenótipo , Reprodução/genética
7.
Cancer Epidemiol Biomarkers Prev ; 29(5): 966-973, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32132150

RESUMO

BACKGROUND: Visceral adipose tissue (VAT) may play a greater role than subcutaneous fat in increasing cancer risk but is poorly estimated in epidemiologic studies. METHODS: We developed a VAT prediction score by regression equations averaged across 100 least absolute shrinkage and selection operator models in a cross-sectional study of 1,801 older adults in the Multiethnic Cohort (MEC). The score was then used as proxy for VAT in case-control studies of postmenopausal breast (950 case-control pairs) and colorectal (831 case-control pairs) cancer in an independent sample in MEC. Abdominal MRI-derived VAT; circulating biomarkers of metabolic, hormonal, and inflammation dysfunctions; and ORs for incident cancer adjusted for BMI and other risk factors were assessed. RESULTS: The final score, composed of nine biomarkers, BMI, and height, explained 11% and 15% more of the variance in VAT than BMI alone in men and women, respectively. The area under the receiver operator curve for VAT >150 cm2 was 0.90 in men and 0.86 in women. The VAT score was associated with risk of breast cancer [OR (95% confidence interval [CI]) by increasing tertiles: 1.00, 1.09 (0.86-1.39), 1.48 (1.16-1.89); P trend = 0.002] but not with colorectal cancer (P = 0.84), although an association [1.00, 0.98 (0.68-1.39), 1.24 (0.88-1.76); P trend = 0.08] was suggested for this cancer after excluding cases that occurred within 7 years of blood draw (P heterogeneity = 0.06). CONCLUSIONS: The VAT score predicted risks of postmenopausal breast cancer and can be used for risk assessment in diverse populations. IMPACT: These findings provide specific evidence for a role of VAT in breast cancer.


Assuntos
Adiposidade/fisiologia , Neoplasias da Mama/epidemiologia , Neoplasias Colorretais/epidemiologia , Gordura Intra-Abdominal/diagnóstico por imagem , Idoso , Biomarcadores/sangue , Índice de Massa Corporal , Neoplasias da Mama/sangue , Neoplasias da Mama/fisiopatologia , Estudos de Casos e Controles , Neoplasias Colorretais/sangue , Neoplasias Colorretais/fisiopatologia , Estudos Transversais , Feminino , Seguimentos , Humanos , Incidência , Imageamento por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Pós-Menopausa/sangue , Pós-Menopausa/fisiologia , Estudos Prospectivos , Medição de Risco/métodos , Medição de Risco/estatística & dados numéricos , Fatores de Risco
8.
Mar Genomics ; 51: 100723, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31784353

RESUMO

High-throughput RNA sequencing (RNA-Seq) has transformed the ecophysiological assessment of individual plankton species and communities. However, the technology generates complex data consisting of millions of short-read sequences that can be difficult to analyze and interpret. New bioinformatics workflows are needed to guide experimentation, environmental sampling, and to develop and test hypotheses. One complexity-reducing tool that has been used successfully in other fields is "t-distributed Stochastic Neighbor Embedding" (t-SNE). Its application to transcriptomic data from marine pelagic and benthic systems has yet to be explored. The present study demonstrates an application for evaluating RNA-Seq data using previously published, conventionally analyzed studies on the copepods Calanus finmarchicus and Neocalanus flemingeri. In one application, gene expression profiles were compared among different developmental stages. In another, they were compared among experimental conditions. In a third, they were compared among environmental samples from different locations. The profile categories identified by t-SNE were validated by reference to published results using differential gene expression and Gene Ontology (GO) analyses. The analyses demonstrate how individual samples can be evaluated for differences in global gene expression, as well as differences in expression related to specific biological processes, such as lipid metabolism and responses to stress. As RNA-Seq data from plankton species and communities become more common, t-SNE analysis should provide a powerful tool for determining trends and classifying samples into groups with similar transcriptional physiology, independent of collection site or time.


Assuntos
Copépodes/genética , Perfilação da Expressão Gênica/métodos , Animais , Feminino , Ontologia Genética , Sequenciamento de Nucleotídeos em Larga Escala , Larva/genética , RNA-Seq , Especificidade da Espécie , Processos Estocásticos , Transcriptoma
9.
Brain Res ; 1641(Pt A): 11-33, 2016 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-26879248

RESUMO

Rapid conduction of nerve impulses is a priority for organisms needing to react quickly to events in their environment. While myelin may be viewed as the crowning innovation bringing about rapid conduction, the evolution of rapid communication mechanisms, including those refined and enhanced in the evolution of myelin, has much deeper roots. In this review, a sequence is traced starting with diffusional communication, followed by transport-facilitated communication, the rise of electrical signaling modalities, the invention of voltage-gated channels and "all-or-none" impulses, the emergence of elongate nerve axons specialized for communication and their fine-tuning to enhance impulse conduction speeds. Finally within the evolution of myelin itself, several innovations have arisen and have been interactively refined for speed enhancement, including the addition and sealing of layers, their limitation by space availability, and the optimization of key parameters: channel density, lengths of exposed nodes and lengths of internodes. We finish by suggesting several design principles that appear to govern the evolution of rapid conduction. This article is part of a Special Issue entitled SI: Myelin Evolution.


Assuntos
Evolução Biológica , Condução Nervosa/fisiologia , Animais , Humanos , Bainha de Mielina/fisiologia
10.
Toxins (Basel) ; 8(1)2016 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-26761033

RESUMO

Despite the medical urgency presented by cubozoan envenomations, ineffective and contradictory first-aid management recommendations persist. A critical barrier to progress has been the lack of readily available and reproducible envenomation assays that (1) recapitulate live-tentacle stings; (2) allow quantitation and imaging of cnidae discharge; (3) allow primary quantitation of venom toxicity; and (4) employ rigorous controls. We report the implementation of an integrated array of three experimental approaches designed to meet the above-stated criteria. Mechanistically overlapping, yet distinct, the three approaches comprised (1) direct application of test solutions on live tentacles (termed tentacle solution assay, or TSA) with single image- and video-microscopy; (2) spontaneous stinging assay using freshly excised tentacles overlaid on substrate of live human red blood cells suspended in agarose (tentacle blood agarose assays, or TBAA); and (3) a "skin" covered adaptation of TBAA (tentacle skin blood agarose assay, or TSBAA). We report the use and results of these assays to evaluate the efficacy of topical first-aid approaches to inhibit tentacle firing and venom activity. TSA results included the potent stimulation of massive cnidae discharge by alcohols but only moderate induction by urine, freshwater, and "cola" (carbonated soft drink). Although vinegar, the 40-year field standard of first aid for the removal of adherent tentacles, completely inhibited cnidae firing in TSA and TSBAA ex vivo models, the most striking inhibition of both tentacle firing and subsequent venom-induced hemolysis was observed using newly-developed proprietary formulations (Sting No More™) containing copper gluconate, magnesium sulfate, and urea.


Assuntos
Ácido Acético/uso terapêutico , Mordeduras e Picadas/tratamento farmacológico , Venenos de Cnidários/toxicidade , Cubomedusas , Ácido Acético/farmacologia , Administração Tópica , Animais , Bioensaio , Eritrócitos/efeitos dos fármacos , Primeiros Socorros , Hemólise/efeitos dos fármacos , Humanos , Nematocisto/efeitos dos fármacos
11.
J Comput Neurosci ; 38(3): 521-38, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25832903

RESUMO

Multilayered, lipid-rich myelin increases nerve impulse conduction velocity, contributes to compact nervous systems, and reduces metabolic costs of neural activity. Based on the hypothesis that increased impulse conduction velocity provides a selective advantage that drives the evolution of myelin, we simulated a sequence of plausible intermediate stages of myelin evolution, each of which providing an enhancement of conduction speed. We started with the expansion of insulating glial coverage, which led first to a single layer of myelin surrounding the axon and then to multiple myelin wraps with well-organized nodes. The myelinated fiber was modeled at three levels of complexity as the hypothesized evolutionary progression became more quantitatively exacting: 1) representing the fiber as a mathematically-tractable uniform active cylinder with the effect of myelination approximated by changing its specific capacitance (C(m)); 2) representing it as a chain of simple, cable-model compartments having alternating nodal and internodal parameters subject to optimization, and 3) representing it in a double cable model with the axon and myelin sheath treated separately. Conduction velocity was optimized at each stage. To maintain optimal conduction velocities, increased myelin coverage of axonal surface must be accompanied by an increase in channel density at the evolving nodes, but along with increases in myelin thickness, a reduction in overall average channel density must occur. Leakage under the myelin sheath becomes more of a problem with smaller fiber diameters, which may help explain the tendency for myelin to occur preferentially in larger nerve fibers in both vertebrates and invertebrates.


Assuntos
Evolução Biológica , Invertebrados/fisiologia , Bainha de Mielina/fisiologia , Vertebrados/fisiologia , Algoritmos , Animais , Axônios/fisiologia , Axônios/ultraestrutura , Simulação por Computador , Modelos Neurológicos , Bainha de Mielina/ultraestrutura , Fibras Nervosas/fisiologia , Condução Nervosa/fisiologia , Neuroglia/fisiologia , Neurônios/fisiologia , Neurônios/ultraestrutura , Temperatura
12.
J Comput Neurosci ; 34(3): 533-46, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23306554

RESUMO

Almost 90 years ago, Lillie reported that rapid saltatory conduction arose in an iron wire model of nerve impulse propagation when he covered the wire with insulating sections of glass tubing equivalent to myelinated internodes. This led to his suggestion of a similar mechanism explaining rapid conduction in myelinated nerve. In both their evolution and their development, myelinating axons must make a similar transition between continuous and saltatory conduction. Achieving a smooth transition is a potential challenge that we examined in computer models simulating a segmented insulating sheath surrounding an axon having Hodgkin-Huxley squid parameters. With a wide gap under the sheath, conduction was continuous. As the gap was reduced, conduction initially slowed, owing to the increased extra-axonal resistance, then increased (the "rise") up to several times that of the unmyelinated fiber, as saltatory conduction set in. The conduction velocity slowdown was little affected by the number of myelin layers or modest changes in the size of the "node," but strongly affected by the size of the "internode" and axon diameter. The steepness of the rise of rapid conduction was greatly affected by the number of myelin layers and axon diameter, variably affected by internode length and little affected by node length. The transition to saltatory conduction occurred at surprisingly wide gaps and the improvement in conduction speed persisted to surprisingly small gaps. The study demonstrates that the specialized paranodal seals between myelin and axon, and indeed even the clustering of sodium channels at the nodes, are not necessary for saltatory conduction.


Assuntos
Potenciais de Ação/fisiologia , Axônios/fisiologia , Modelos Neurológicos , Fibras Nervosas Mielinizadas/fisiologia , Condução Nervosa/fisiologia , Animais , Simulação por Computador , Bainha de Mielina
13.
Biol Cybern ; 90(4): 280-90, 2004 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-15085347

RESUMO

The ability to correct parameters of voltage-gated conductances measured under poor spatial control by point voltage clamp could rescue much flawed experimental data. We explore a strategy for correcting errors in experiments that employs a full-trace approach to parameter determination. Simulated soma voltage-clamp runs are made on a model neuron with a single voltage-gated, Hodgkin-Huxley channel type distributed uniformly along an elongate process. Estimates for both kinetic and I(V) parameters are obtained by fitting a form of the Hodgkin-Huxley equations to the complete time course of leak-subtracted current curves. The fitted parameters are used to determine how much correction in each parameter is needed to regenerate the set actually belonging to the channel. Corrections are generated for a range of neurite lengths, conductance densities, and channel characteristics.


Assuntos
Potenciais de Ação/fisiologia , Dendritos/fisiologia , Condutividade Elétrica , Modelos Neurológicos , Neurônios/citologia , Animais , Simulação por Computador , Ativação do Canal Iônico/fisiologia , Cinética , Técnicas de Patch-Clamp/métodos , Fatores de Tempo
14.
J Comput Neurosci ; 14(3): 253-69, 2003.
Artigo em Inglês | MEDLINE | ID: mdl-12766427

RESUMO

Significant error is made by using a point voltage clamp to measure active ionic current properties in poorly space-clamped cells. This can even occur when there are no obvious signs of poor spatial control. We evaluated this error for experiments that employ an isochronal I(V) approach to analyzing clamp currents. Simulated voltage clamp experiments were run on a model neuron having a uniform distribution of a single voltage-gated inactivating ionic current channel along an elongate, but electrotonically compact, process. Isochronal Boltzmann I(V) and kinetic parameter values obtained by fitting the Hodgkin-Huxley equations to the clamp currents were compared with the values originally set in the model. Good fits were obtained for both inward and outward currents for moderate channel densities. Most parameter errors increased with conductance density. The activation rate parameters were more sensitive to poor space clamp than the I(V) parameters. Large errors can occur despite "normal"-looking clamp curves.


Assuntos
Potenciais de Ação/fisiologia , Membrana Celular/fisiologia , Potenciais Pós-Sinápticos Excitadores/fisiologia , Canais Iônicos/fisiologia , Neuritos/fisiologia , Transmissão Sináptica/fisiologia , Animais , Artefatos , Humanos , Cinética , Modelos Neurológicos , Condução Nervosa/fisiologia , Técnicas de Patch-Clamp/métodos , Tempo de Reação/fisiologia , Reprodutibilidade dos Testes
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