Tree regeneration characteristics in limestone forests of the Cat Ba National Park, Vietnam

Background The ability of overstory tree species to regenerate successfully is important for the preservation of tree species diversity and its associated flora and fauna. This study investigated forest regeneration dynamics in the Cat Ba National Park, a biodiversity hotspot in Vietnam. Data was collected from 90 sample plots (500 m2) and 450 sub-sample plots (25 m2) in regional limestone forests. We evaluated the regeneration status of tree species by developing five ratios relating overstory and regeneration richness and diversity. By examining the effect of environmental factors on these ratios, we aimed to identify the main drivers for maintaining tree species diversity or for potential diversity gaps between the regeneration and the overstory layer. Our results can help to increase the understanding of regeneration patterns in tropical forests of Southeast Asia and to develop successful conservation strategies. Results We found 97 tree species in the regeneration layer compared to 136 species in the overstory layer. The average regeneration density was 3764 ± 1601 per ha. Around 70% of the overstory tree species generated offspring. According to the International Union for Conservation of Nature’s Red List, only 36% of threatened tree species were found in the regeneration layer. A principal component analysis provided evidence that the regeneration of tree species was slightly negatively correlated to terrain factors (percentage of rock surface, slope) and soil properties (cation exchange capacity, pH, humus content, soil moisture, soil depth). Contrary to our expectations, traces of human impact and the prevailing light conditions (total site factor, gap fraction, openness, indirect site factor, direct site factor) had no influence on regeneration density and composition, probably due to the small gradient in light availability. Conclusion We conclude that the tree species richness in Cat Ba National Park appears to be declining at present. We suggest similar investigations in other biodiversity hotspots to learn whether the observed trend is a global phenomenon. In any case, a conservation strategy for the threatened tree species in the Cat Ba National Park needs to be developed if tree species diversity is to be maintained.

Microsites Influence the Light Response of Young Douglas-Fir (Pseudotsuga menziesii (Mirb.) Franco)

Two comparable sites with uneven-aged mixed forest stands with more than 20% Douglas-fir in the growing stock at an altitude of 650 m a.s.l. were selected. The physiological response of young trees to different light intensities was measured during the main growing season in three consecutive years, and four different light categories, which were determined from hemispherical photographs. The four light intensity categories were defined according to Indirect Site Factor (ISF%): in the open (A-ISF > 35%), at the outer forest edge (B-25% < ISF < 35%), at the inner forest edge (C-15% < ISF < 25%), and under complete canopy under mature forest stand (D-ISF < 15%). Climate data were obtained from the Royal Netherlands Meteorological Institute ‘Climate Explorer’ website (http://climexp.knmi.nl). For the intensive micrometeorological observations, four monitoring sites were established along the elevation gradient at each site during summer and late fall to record relative humidity (RH%) and temperature (°C) with a 30 min recording interval sequence. Measured assimilation responses (A) and light use efficiency () at one site followed the expected pattern, while humidity combined with microsite conditions proved significant in explaining the specific response of young Douglas-fir to the different light intensity at the other site. For higher survival and optimal future development of Douglas-fir in the changing environment, microsites with higher capacity for storage moisture and favorable microclimate should generally be preferred to exposed and dry sites.

Adaptation and Agronomic Performance of Domesticated Moroccan Oat (Avena magna ssp. domestica) Lines under Subsistence Farming Conditions at Multiple Locations in Morocco

Common hexaploid oat (Avena sativa L.) is an important global cereal crop. A Moroccan tetraploid sister species, A. magna Murphy et Terrel, was exclusively a wild species until recently. The goal of domestication was to exploit its superior groat-protein content and climatic tolerances. We set up replicated trials of 41 domesticated A. magna lines on eight Moroccan farms during the 2017–18 and 2018–19 growing seasons. Twenty traits were measured and analyses of variance detected significant differences among lines. The highest grain yield was at Berrechid in 2017–18 (63.56 q/ha), with an average annual yield across sites of 43.50 q/ha, the site factor explaining 82% and the genotype-environment interaction explaining 15% of the variability. In the second year, El Kebab recorded the highest yield at 20.03 q/ha over the annual average of 14.78 q/ha. In this second year, the site factor was highly significant, explaining 42.25% of the variation, with the genotype-environment interaction explaining 26.61% of the variability. An additional main effect and multiplicative interaction analysis of the eight two-year trials identified several accessions with good yield stability. Twelve lines exhibited a ASVs ≤ 1.50, with five accessions (A34, A40, A23, A05, A04) exceeding the overall average yield of 29.53 and A34 having the greatest mean grain yield and stability. The versatility and stability of A. magna can provide a sustainable protein source and an economic resource for farmers seeking products that are resilient to climatic instability.

Site Soil Classification Interpretation Based on Standard Penetration Test and Shear Wave Velocity Data

Site soil classification provides vital information for predicting the soil amplification or the site factor. The site factor is important for calculating the surface spectral acceleration in the seismic design of buildings. Based on the Indonesian seismic code, site soil classification can be conducted by calculating the average standard penetration (N-SPT) resistance, the average shear wave velocity (VS) and the average undrained soil strength (Su) of the upper 30 m of a subsoil layer. Different results may be obtained at the same location when the site soil classification is predicted using N-SPT than when using VS data. The restriction of N-SPT values until a maximum of 60 compared to a VS maximum of 750 m/sec can produce different soil classes and will directly impact the calculation of the surface spectral acceleration. This paper describes the different results of site soil classification prediction calculated using the average N-SPT and the average VS, conducted at Semarang City, Indonesia. Site soil classification maps developed based on both datasets are also presented, to evaluate the different site soil classification distributions. Only soil classes SD and SE were observed using N-SPT maximum 60, whereas soil classes SC, SD and SE were observed using N-SPT maximum 120.

Structure of Gcn1 bound to stalled and colliding 80S ribosomes

The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for the kinase Gcn2, which in turn is activated by stalled ribosomes, leading to phosphorylation of eIF2 and a subsequent global repression of translation. The fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, a negative regulator of Gcn2. Despite the wealth of available biochemical data, information on structures of Gcn proteins on the ribosome has remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the P-stalk and the A-site region of the lead ribosome. The lead ribosome is stalled in a nonrotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, and Rbg2/Gir2 in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site, and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings reveal the interaction mode of the Gcn2-activating protein Gcn1 with colliding ribosomes and provide insight into the regulation of Gcn2 activation. The binding of Gcn1 to a disome has important implications not only for the Gcn2-activated ISR, but also for the general ribosome-associated quality control pathways.

Tree Regeneration Characteristics in Limestone Forests of the Cat Ba National Park, Vietnam

Background: Forest regeneration is decisive for future forest development and therefore of major concern to forest ecologists. The ability of overstory tree species to regenerate successfully is important for the preservation of tree species diversity and its associated flora and fauna. This study investigated forest regeneration dynamics in the Cat Ba National Park, a biodiversity hotpot in Vietnam. Data was collected from 90 sample plots and 450 sub-sample plots in the regional limestone forests. We compared species richness between the regeneration and overstory tree layers and examined the effect of environmental factors on the occurrence of regeneration. We developed five ratios to relate overstory and regeneration richness and diversity. Results: We found 97 tree species in the regeneration layer compared to 136 species in the overstory layer. Average regeneration density was 3,764 ± 1,601 per ha. Around 70% of the overstory tree species generated offspring. Of the tree species threatened according to The International Union for Conservation of Nature’s Red List of Threatened Species, only 36% were found in the regeneration layer. A principal component analysis provided evidence that the regeneration of tree species was linked to terrain factors (percentage of rock surface, slope) and soil properties (Cation exchange capacity, pH, humus content, soil moisture, soil depth). Contrary to our expectations, the prevailing light conditions (total site factor, gap fraction, openness, indirect site factor, direct site factor) had no influence on regeneration density and composition, probably due to the small gradient in light availability. Conclusion: We conclude that tree species richness in Cat Ba National Park appears to be declining at present. We suggest similar investigations in other biodiversity hotspots to learn whether the observed trend is a global phenomenon. In any case, a conservation strategy for the threatened tree species in the Cat Ba National Park needs to be developed if tree species diversity is to be maintained.

Evaluation of hemispherical photos extracted from smartphone spherical panorama images to estimate canopy structure and forest light environment

Hemispherical photography (HP) is one of the most commonly employed methods to estimate forest canopy structure and understory light environments. Traditional methods require expensive, specialized equipment, are tedious to deploy, and are sensitive to exposure settings. In contrast, modern smartphone cameras are readily available and make use of ever-improving software to produce images with high dynamic range and clarity, but lack suitable hemispherical lenses. Thus, despite the fact that almost all ecologists and foresters carry a high-powered, image processing device in our pockets, we have yet to fully employ it for the purpose of data collection. As an alternative, hemispherical images can be extracted from spherical panoramas produced by many smartphone camera applications. I compared hemispherical photos captured with a digital single lens reflex camera and 180° lens to those extracted from smartphone spherical panoramas (SSP) for 72 sites representing a range of canopy types and densities. I estimated common canopy and light measures (canopy openness, leaf area index, and global site factor) as well as image quality measures (total gap area, number of gaps, and relative gap size) to compare methods. The SSP HP method leverages built-in features of current generation smartphones including exposure metering over restricted field-of-view, high dynamic range tonal correction, computational sharpening, high pixel density, and automatic leveling via the phone’s built-in gyroscope to yield an accurate alternative to traditional HP in canopy estimation. Although the process of stitching together multiple photos occasionally produces artifacts in the SSP HP images, estimates of canopy openness and global site factor are highly correlated with those of traditional methods (R2> 0.9) and are comparable to under- or over-exposing traditional HP by 1-1.5 stops. In addition to superior image quality, SSP HP requires no additional equipment or exposure settings and is likely to prove more robust to uneven lighting conditions by avoiding wide-angles lenses and exploiting HDR images.

Structure of Gcn1 bound to stalled and colliding 80S ribosomes

Protein synthesis is essential to cells and requires a constant supply of nutrients. Amino acid starvation leads to accumulation of uncharged tRNAs that promote ribosomal stalling, which is sensed by the protein kinase Gcn2, together with its effector proteins, Gcn1 and Gcn20. Activation of Gcn2 phosphorylates eIF2, leading to a global repression of translation. Fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, which is a negative regulator of Gcn2. Despite the wealth of biochemical data, structures of Gcn proteins on the ribosome have remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the A-site region of the lead ribosome. The lead ribosome is stalled in a non-rotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, as well as Rbg2/Gir2 located in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings provide a structural basis for Rbg2/Gir2 repression of Gcn2, and also reveal that colliding disomes are the substrate for Gcn1 binding, which has important implications not only for Gcn2-activated stress responses, but also for general ribosome quality control (RQC) pathways.

Reliability and Validity of the Arabic Version of a Questionnaire Assessing Pain, Discomfort and Related Jaw Function Impairment after Extraction of Primary Teeth in Children

This study aims to translate a previously published English language questionnaire that assessed pain and discomfort after the extraction of primary teeth in children into Arabic, and evaluate its validity and reliability. All participating children (n = 120), aged 9 to 12-years-old, completed the 33-item Arabic version questionnaire after the extraction procedure had taken place. The questionnaire included three parts that were completed at three different times, namely, immediately, the first evening, and one week after the extraction procedure. Internal consistency, content validity, criterion validity, and factor analysis were performed. The results showed a good internal consistency (Cronbach’s alpha = 0.83), acceptable criterion validity with a significantly strong correlation with the Visual Analog Scale (VAS), and satisfactory content validity (average content validity index (CVI = 0.90). The final factor model was comprised of four factors with an eigenvalue greater than 1, explaining 70% of the common variance. The identified factors were labeled as follows: Factor 1—analgesic consumption; Factor 2—expression of discomfort from the extraction site; Factor 3—perception of masticatory capability; and Factor 4—pain/discomfort from the dental extraction procedure. Based on the results, a shorter form of the questionnaire had satisfactory psychometric characteristics and can be used with children within the selected age group.

A Protein in the Yeast Saccharomyces cerevisiae Presents DNA Binding Homology to the p53 Checkpoint Protein and Tumor Suppressor

Saccharomyces cerevisiae does not contain a p53 homolog. Utilizing this yeast as an in vivo test tube model, our aim was to investigate if a yeast protein would show p53 DNA binding homology. Electrophoretic mobility shift analyses revealed the formation of specific DNA-protein complexes consisting of S. cerevisiae nuclear protein(s) and oligonucleotides containing p53 DNA binding sites. A S. cerevisiae p53 binding site factor (Scp53BSF) bound to a p53 synthetic DNA-consensus sequence (SCS) and a p53 binding-site sequence from the MDM2 oncogene. The complexes were of comparable size. Like mammalian p53, the affinity of Scp53BSF for the SCS oligonucleotide was higher than for the MDM2 oligonucleotide. Binding of Scp53BSF to the SCS and MDM2 oligonucleotides was strongly competed by unlabeled oligonucleotides containing mammalian p53 sites, but very little by a mutated site oligonucleotide. Importantly, Scp53BSF-DNA binding activity was significantly induced in extracts from cells with DNA damage. This resulted in dose-dependent coordinated activation of transcription when using p53-binding site reporter constructs. An ancient p53-like DNA binding protein may have been found, and activation of DNA-associated factors to p53 response elements may have functions not yet determined.