Transcriptional and epigenetic landscape of Ca2+-signaling genes in hepatocellular carcinoma

Calcium (Ca²⁺) signaling has a major role in regulating a wide range of cellular mechanisms, including gene expression, proliferation, metabolism, cell death, muscle contraction, among others. Recent evidence suggests that ~ 1600 genes are related to the Ca²⁺ signaling. Some of these genes’ expression is altered in several pathological conditions, including different cancer types, and epigenetic mechanisms are involved. However, their expression and regulation in hepatocellular carcinoma (HCC) and the liver are barely known. Here, we aimed to explore the expression of genes involved in the Ca²⁺-signaling in HCC, liver regeneration, and hepatocyte differentiation, and whether their expression is regulated by epigenetic mechanisms such as DNA methylation and histone posttranslational modifications (HPM). Results show that several Ca²⁺-signaling genes’ expression is altered in HCC samples; among these, a subset of twenty-two correlate with patients’ survival. DNA methylation correlates with eight of these genes’ expression, and Guadecitabine, a hypomethylating agent, regulates the expression of seven down-regulated and three up-regulated genes in HepG2 cells. The down-regulated genes displayed a marked decrease of euchromatin histone marks, whereas up-regulated genes displayed gain in these marks. Additionally, the expression of these genes is modulated during liver regeneration and showed similar profiles between in vitro differentiated hepatocytes and liver-derived hepatocytes. In conclusion, some components of the Ca²⁺-signaling are altered in HCC and displayed a correlation with patients’ survival. DNA methylation and HMP are an attractive target for future investigations to regulate their expression. Ca²⁺-signaling could be an important regulator of cell proliferation and differentiation in the liver.Electronic supplementary materialThe online version of this article (10.1007/s12079-020-00597-w) contains supplementary material, which is available to authorized users.     

Integrating ecological and biogeographical tools for the identification of conservation areas in two Neotropical biogeographic provinces in Argentina based on phytophagous insects

Biodiversity and Conservation - The Chaco and Pampean provinces in the Neotropical region are highly disturbed by intensive forestry and livestock raising. This study is an integrative approach...     

Antifungal and Insecticidal Activities of Selected Plant Species from Cloud Forest of Veracruz,Mexico: A Contribution to the Search of Novel Control Agents against Ambrosia Pest Complexes

The antifungal and insecticidal activities of 34 extracts from 27 plant species were evaluated against fungal phytopathogens of the genus Fusarium and Xyleborus Scolytine ambrosia beetles involved in Fusarium dieback (FD) and laurel wilt (LW) diseases. Sixteen extracts caused mycelial growth inhibition (MGI) above 23 % at 2 mg mL⁻¹ against F. solani, those from S. nudum and M. argyrophylla exhibited the highest MGI (57 % and 49 %, respectively). Thirteen extracts displayed significant antifungal activity against F. kuroshium, those from C. nocturnum and M. argyrophylla exhibited the highest MGI (100 % and 54.9 %, respectively). Additionally, ten plants extracts caused mortality in at least one of the beetle species tested, mainly from Solanaceae species. In the most active species, 39 phenolics were identified that may have contributed to their biological effects. This study is one of the first to report the potential of plant-derived natural products against the causative agents of FD and LW.     

Typical cyperoid reproductive structures in Lipocarpha humboldtiana and Ascolepis brasiliensis (Cypereae – Cyperoideae – Cyperaceae): New evidence from a development perspective

Ascolepis and Lipocarpha, Cyperaceae, have highly reduced reproductive structures and hypogynous scales that are controversially appreciated. Because of this, flowers and spikelets and, thus, inflorescences have been interpreted in different ways, which, in turn, has led to placing the two genera in different tribes. Some authors interpret spikelets in Ascolepis and Lipocarpha as many-flowered and the so-called hypogynous scales as homologous to the lateral scales of Hypolytrum, or consider these scales comparable to a Scirpus bristle. However, many other authors consider spikelets in Lipocarpha and Ascolepis to be a result of a reductional process from a many-flowered cyperoid spikelet to a single-flowered spikelet, where the adaxial and abaxial hypogynous scales may be seen as the respective prophyll and glume of the reduced spikelets. The latest molecular phylogenies of Cyperaceae show both genera nested in the Cyperus clade, forming, in turn, a clade together with the rest of the Cypereae genera having single-flowered spikelets and hypogynous scales. Alternatively, based on this, the scales of uncertain homology that accompany the Ascolepis and Lipocarpha flower might be seen as special reproductive formations, representing a synapomorphy of such clade, instead of relicts of an ancestor with many-flowered spikelets. In view of this, freshly collected inflorescences of Lipocarpha humboldtiana Nees and Ascolepis brasiliensis (Kunth) Benth. ex C. B. Clarke were studied using light and scanning electron microscopy, with the aim of elucidating the nature of the controversially interpreted reproductive structures of these species from a development perspective. Results show that the “hypogynous scales” simply represent vestigial structures derived from the reduction of typical cyperoid spikelets, rather than a perianth part or specialized formations emerging as evolutionary novelties. Two scales are typically generated in both species, one being abaxial and the other adaxial, homologous to a glume and a prophyll, respectively, which contrasts with the eprophyllate condition so far attributed to Ascolepis. In both cases, the inflorescence is a spike of reduced spikelets, and the floral development in L. humboldtiana and in A. brasiliensis follows the general ontogenetic pattern observed in Cyperoideae. These characteristics support the inclusion of both genera in the Cypereae tribe.     

Evaluation of different peptide fragmentation types and mass analyzers in data‐dependent methods using an Orbitrap Fusion Lumos Tribrid mass spectrometer

One of the major additions in MS technology has been the irruption of the Orbitrap mass analyzer, which has boosted the proteomics analyses of biological complex samples since its introduction. Here, we took advantage of the capabilities of the new Orbitrap Fusion Lumos Tribrid mass spectrometer to assess the performance of different data‐dependent acquisition methods for the identification and quantitation of peptides and phosphopeptides in single‐shot analysis of human whole cell lysates. Our study explored the capabilities of tri‐hibrid mass spectrometers for (phospho‐) peptide identification and quantitation using different gradient lengths, sample amounts, and combinations of different peptide fragmentation types and mass analyzers. Moreover, the acquisition of the same complex sample with different acquisition methods resulted in the generation of a dataset to be used as a reference for further analyses, and a starting point for future optimizations in particular applications.     

Alterations in growth and crassulacean acid metabolism (CAM) activity of in vitro cultured cactus

Unlike C-3 plants, cacti possess a crassulacean acid metabolism (CAM) physiology that can alter the pattern of carbon uptake and affect plant growth under artificial environmental conditions, especially in tissue culture. In vitro-derived plantlets of Coryphantha minima grew 7-fold larger than plants cultured under similar ex vitro conditions. Growth regulators incorporated into the culture media during shoot proliferation stage of micropropagation had a strong influence on this increased growth. Other important factors that contributed to increased growth under in vitro conditions were high relative humidity and sugar in the culture medium. An analysis of gas exchange and daily fluctuations of malic acid levels revealed an increase in net photosynthetic rate, in terms of carbon assimilation, by in vitro plants compared with that of ex vitro plants. This stimulated photosynthesis in the presence of an external carbon source was unexpected but apparently true for cacti exhibiting CAM physiology. Unlike CAM plants grown in ex vitro conditions, net CO₂ uptake by in vitro-cultured cacti occurred continuously in the light as well as the dark. Once regenerated, cacti were transferred to ex vitro conditions where the normal CAM pathway resumed with a concomitant reduction in growth and CO₂ uptake. These results showed that growth of cacti can be considerably accelerated by in vitro culture. This revised version was published online in June 2006 with corrections to the Cover Date.     

Canola and Oat Forage Potential Evaluation in Four Early Planting Dates

Canola and oat forage potential may be affected by climatic conditions when sown early. The objective of this study was to evaluate the forage canola and oat potential in four early sowing dates (September 11 and 25; October 9 and 23) during the 2012-2013 and 2013-2014 cycles in Matamoros, Coahuila, Mexico. Growth cycle duration, chemical composition, dry matter (DM), crude protein (CP), and net energy for lactation (NE_L) yields were determined. High temperatures and long photoperiods affected crops seeded on September 11, accelerating growth and reducing canola (26.6%-31.7%) and oat (15.8%) DM yields. As of September 25, canola cv IMC 205 reached DM yields (7746 kg ha^-1 -9276 kg ha^-1 ) similar to those obtained by oat (8115 kg ha^-1 -9507 kg ha^-1 ), while canola cv Hyola 401 obtained such yields only until October 23. Canola chemical composition was better than that found in oat, with higher CP, but lower acid detergent fiber (ADF) and neutral detergent fiber (NDF) contents. Canola equaled oat CP yields (972 kg ha^-1 -1215 kg ha^-1 ) in the first sowing date, while in the other three other canola sowings reached higher yields (1193 kg ha^-1 -1889 kg ha^-1 ). As for NEL yields, no difference was observed between both species. The best sowing date for canola is from September 25 on, with CP production advantages over oat.