An analysis of determinants of amino acids substitution rates in bacterial proteins

The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated in comparative analyses. To this aim, we made regression analyses combining data available on these variables and on evolutionary rates, in two well-documented model bacteria, Escherichia coli and Bacillus subtilis. In both bacteria, the level of expression of the protein in the cell was by far the most important driving force constraining the amino acids substitution rate. Subsequent inclusion in the analysis of the other variables added little further information. Furthermore, when the rates of synonymous substitutions were included in the analysis of the E. coli data, only the variable expression levels remained statistically significant. The rate of nonsynonymous substitution was shown to correlate with expression levels independently of the rate of synonymous substitution. These results suggest an important direct influence of expression levels, or at least codon usage bias for translation optimization, on the rates of nonsynonymous substitutions in bacteria. They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes.     

Fish biodiversity of Saint Peter and Saint Paulʼs Archipelago,Mid-Atlantic Ridge,Brazil: new records and a species database

Saint Peter and Saint Paul's Archipelago (SPSPA), one of the smallest and most isolated island groups in the world, is situated on the Mid-Atlantic Ridge, between Brazil and the African continent. SPSPA has low species richness and high endemism; nonetheless, the diversity of fishes from deep habitats (>30 m depth) had not been previously studied in detail. Several expeditions conducted between 2009 and 2018 explored the shallow and deep reefs of SPSPA using scuba, closed-circuit rebreathers, manned submersibles, baited remote underwater stereo-videos (stereo-BRUV) and fishing between 0 and 1050 m depth. These expeditions yielded 41 new records of fishes for SPSPA: 9 in open waters, 9 in shallow waters (0–30 m), 8 in mesophotic ecosystems (30–150 m) and 15 in deeper reefs (>150 m). Combined with literature records of adult pelagic, shallow and deep-reef species, as well as larvae, the database of the fish biodiversity for SPSPA currently comprises 225 species (169 recorded as adult fishes and 79 as larvae, with 23 species found in both stages). Most of them (112) are pelagic, 86 are reef-associated species and 27 are deep-water specialists. Species accumulation curves show that the number of fish species has not yet reached an asymptote. Whereas the number of species recorded in SPSPA is similar to that in other oceanic islands in the Atlantic Ocean, the proportion of shorefishes is relatively lower, and the endemism level is the third highest in the Atlantic. Twenty-nine species are listed as threatened with extinction. Observations confirm the paucity of top predators on shallow rocky reefs of the island, despite the presence of several pelagic shark species around SPSPA. Because all of the endemic species are reef associated, it is argued that the new marine-protected areas created by the Brazilian government do not ensure the protection and recovery of SPSPA's biodiversity because they allow exploitation of the most vulnerable species around the archipelago itself. This study suggests a ban on reef fish exploitation inside an area delimited by the 1000 m isobath around the islands (where all known endemics are concentrated) as the main conservation strategy to be included in the SPSPA management plan being prepared by the Brazilian government.     

Reversibility of H+-ATPase and H+-Pyrophosphatase in Tonoplast Vesicles from Maize Coleoptiles and Seeds

Tonoplast-enriched vesicles isolated from maize (Zea mays L.) coleoptiles and seeds synthesize ATP from ADP and inorganic phosphate (Pi) and inorganic pyrophosphate from Pi. The synthesis is consistent with reversal of the catalytic cycle of the H⁺-ATPase and H⁺-pyrophosphatase (PPase) vacuolar membrane-bound enzymes. This was monitored by measuring the exchange reaction that leads to ³²Pi incorporation into ATP or inorganic pyrophosphate. The reversal reactions of these enzymes were dependent on the proton gradient formed across the vesicle membrane and were susceptible to the uncoupler carbonyl cyanide p(trifluoromethoxy)-phenylhydrazone and the detergent Triton X-100. Comparison of the two H⁺ pumps showed that the H⁺-ATPase was more active than H⁺-PPase in coleoptile tonoplast vesicles, whereas in seed vesicles H⁺-PPase activity was clearly dominant. These findings may reflect the physiological significance of these enzymes in different tissues at different stages of development and/or differentiation.     

Sustained sensitivity modifications induced by brief length perturbations in the crayfish slowly adapting stretch receptor

These experiments in the slowly adapting stretch receptor of crayfish test the effects of brief length perturbations (i.e., pulses) when presented in isolation at different constant elongations or superimposed on trapezoidal stretches of different amplitudes. Within "in vivo" lengths, during static responses, perturbations reduced firing rates to below control values and, in extreme cases, could silence the receptor. This effect, or "down-step," was sustained, occurred above a threshold pulse amplitude and background stretch, and increased with both stimulus characteristics, but was not present during dynamic responses. Beyond "in vivo" lengths, and in a few cases within those limits but close to the extremes, the receptor was silent but perturbations could restore activity. Lengthening pulses were more effective than shortening ones in generating after-effects. Perturbations change, during indefinitively long periods, the receptor's length or static sensitivity acting as a negative feedback which tends to maintain the discharge rate within fixed values. Perturbations disclose marked nonlinearities, which suggest that the classical view of a proportional control in the reflex loop in which the receptor participates may not operate in natural conditions.     

Verrucomicrobia subdivision 1 strains display a difference in the colonization of the leek (Allium porrum) rhizosphere

Strains CHC12 and CHC8, belonging to, respectively, Luteolibacter and Candidatus genus Rhizospheria (Verrucomicrobia subdivision 1), were recently isolated from the leek rhizosphere. The key question addressed in this study was: does attraction to and colonization of the rhizosphere occur in the same way for both strains? Therefore, the fate of the two strains was studied near in vitro-grown leek roots and in soil zones proximate to and at a further distance from roots in a model plant-soil microcosm set-up. Quantitative PCR detection with specific primers was used, as the cultivation of these bacteria from soil is extremely fastidious. The data indicated that natural populations of Luteolibacter (akin to strain CHC12) had lower numbers in the rhizosphere than in the corresponding bulk soil. On the other hand, the populations of Candidatus genus Rhizospheria, i.e. strain CHC8, showed higher numbers in the rhizosphere than in the bulk soil. Increased strain CHC8 cell-equivalent numbers in the rhizosphere were not only the result of in situ cell multiplication, but also of the migration of cells towards the roots. Luteolibacter and Candidatus genus Rhizospheria cells displayed differences in attraction to the rhizosphere and colonization thereof, irrespective of the fact that both belonged to Verrucomicrobia subdivision 1.     

The Galactose-Binding Lectin Isolated from Vatairea macrocarpa Seeds Enhances the Effect of Antibiotics Against Staphylococcus aureus–Resistant Strain

Probiotics and Antimicrobial Proteins - The use of natural products together with standard antimicrobial drugs has recently received more attention as a strategy to combat infectious diseases...     

From endosperm to triploid plants: a stepwise characterization of the de novo shoot organogenesis and morpho-agronomic aspects of an ornamental passion fruit (Passiflora foetida L.)

Plant Cell, Tissue and Organ Culture (PCTOC) - Somaclonal variation during in vitro culture is often an undesirable phenomenon but may also be a source of genetic variation useful for breeders. The...     

Computer-Guided Trypanocidal Activity of Natural Lactones Produced by Endophytic Fungus of Euphorbia umbellata

Hundreds of millions of people worldwide are affected by Chagas’ disease caused by Trypanosoma cruzi. Since the current treatment lack efficacy, specificity, and suffers from several side-effects, novel therapeutics are mandatory. Natural products from endophytic fungi have been useful sources of lead compounds. In this study, three lactones isolated from an endophytic strain culture were in silico evaluated for rational guidance of their bioassay screening. All lactones displayed in vitro activity against T. cruzi epimastigote and trypomastigote forms. Notably, the IC₅₀ values of (+)-phomolactone were lower than benznidazole (0.86 vs. 30.78 μM against epimastigotes and 0.41 vs. 4.88 μM against trypomastigotes). Target-based studies suggested that lactones displayed their trypanocidal activities due to T. cruzi glyceraldehyde-3-phosphate dehydrogenase (TcGAPDH) inhibition, and the binding free energy for all three TcGAPDH-lactone complexes suggested that (+)-phomolactone has a lower score value (−3.38), corroborating with IC₅₀ assays. These results highlight the potential of these lactones for further anti-T. cruzi drug development.     

Relationship between ventilatory threshold and muscle fiber conduction velocity responses in trained cyclists

The relationship between surface electromyography (SEMG) amplitude and the ventilatory threshold has been extensively studied. However, previous studies of muscle fiber conduction velocity (MFCV) are scarce and present insufficient evidence concerning the relationship between MFCV and metabolic responses during cycling. Based on that fact, the purpose of this study is twofold: (1) to investigate the existence of a MFCV threshold (MFCVT) during cycling and (2) to verify if this possible breakpoint is correlated with the ventilatory threshold (VT) and the SEMG threshold (SEMGT). Eight trained male cyclists (age 36.0 ± 9.7 years) performed an incremental cycling test with initial workload of 150 W gradually incremented by 20 W min^?1 until the exhaustion. Gas analyses were conducted using a breath-by-breath open-circuit spirometry and SEMG were registered from vastus lateralis in each pedaling cycle with a linear array of electrodes. A bi-segmental linear regression computer algorithm was used to estimate VT, MFCVT and SEMGT respectively in the carbon dioxide production (VCO₂), MFCV and electromyography root mean square (EMG RMS) curves. The one way ANOVA for repeated measures did not reveal any significant difference among VT (77.1 ± 7.5% of VO₂max), MFCVT (80.3 ± 10.4% of VO₂max) and SEMGT (81.9 ± 11.7% of VO₂max). The Bland and Altman procedure confirmed a good concordance between SEMGT and VT (Bias = 5.5 of %VO₂max) as well as MFCVT and VT (Bias = 5.2 of %VO₂max). The present findings suggest that muscle fiber conduction velocity threshold is a valid and reliable non-invasive tool to obtain information about ventilatory threshold in trained cyclists.