bluuebunny/crossref_metadata_2025 huggingface dataset:
Climate Change Effects on Height–Diameter Allometric Relationship Vary with Tree Species and Size for Larch Plantations in Northern and Northeastern China
Authors: Xu Qigang , Lei Xiangdong , Zang Hao , Zeng Weisheng
Published: March 2022

Tree height–diameter relationship is very important in forest investigation, describing forest structure and estimating carbon storage. Climate change may modify the relationship. However, our understanding of the effects of climate change on the height–diameter allometric relationship is still limited at large scales. In this study, we explored how climate change effects on the relationship varied with tree species and size for larch plantations in northern and northeastern China. Based on the repeated measurement data of 535 plots from the 6th to 8th national forest inventory of China, climate-sensitive tree height–diameter models of larch plantations in north and northeast China were developed using two-level nonlinear mixed effect (NLME) method. The final model was used to analyze the height–diameter relationship of different larch species under RCP2.6, RCP 4.5, and RCP8.5 climate change scenarios from 2010 to 2100. The adjusted coefficient of determination Radj2, mean absolute error (MAE) and root mean squared error (RMSE) of the NLME models for calibration data were 0.92, 0.76 m and 1.06 m, respectively. The inclusion of climate variables mean annual temperature (MAT) and Hargreaves climatic moisture deficit (CMD) with random effects was able to increase Radj2 by 19.5% and reduce the AIC (Akaike’s information criterion), MAE and RMSE by 22.2%, 44.5% and 41.8%, respectively. The climate sensitivity of larch species was ranked as L. gmelinii > the unidentified species group > L. principis > L. kaempferi > L. olgensis under RCP4.5, but L. gmelinii > L. principis > the unidentified species group > L. olgensis > L. kaempferi under RCP2.6 and RCP8.5. Large trees were more sensitive to climate change than small trees.
Differences in Growth–Climate Relationships among Scots Pines Growing on Various Dune Generations on the Southern Baltic Coast
Authors: Cedro Anna , Cedro Bernard , Podlasiński Marek
Published: March 2022

This study focuses on analyzing the growth rate and growth–climate relationship in Scots pine (Pinus sylvestris L.) growing on coastal dunes of different ages on the Southern Baltic coast. Podzols have developed on these dunes. Depending on dune age, however, podzols are characterized by a different degree of development and richness, which represents the main factor differentiating the studied habitats: the oldest brown dunes (BD), younger yellow dunes (YD), and the youngest white dunes (WD). Samples were taken from 68 trees using Pressler borers. Using classic cross-dating methods, local chronologies were compiled that served as the basis for further analyses. Basic analyses of soil properties were also performed. Trees growing on brown dunes display the widest tree-rings and the highest rate of cumulative radial growth. Both rates are the lowest for trees growing on white dunes (WD). The dominant meteorological factor shaping tree-ring widths is late winter/early spring air temperature (February/March). However, in poorer habitats with inferior soil air–water conditions, rainfall sums and rainfall distribution through the year become progressively more significant factors. On white dunes (WD), the strongest growth–climate correlations are obtained for summer precipitation. These results identify habitat richness as the main factor shaping growth dynamics in Scots pines growing on dunes. Due to the protective function of the studied tree stands (coast protection), and in light of the rising sea levels and increasing storm intensities, further studies are required, aiming at understanding all interrelationships occurring in these valuable ecosystems.
Optimization of Forest Management in Large Areas Arising from Grouping of Several Management Bodies: An Application in Northern Portugal
Authors: Cabral Margarida , Fonseca Teresa Fidalgo , Cerveira Adelaide
Published: March 2022

The success of forest management towards achieving desired outcomes depends on various factors and can be improved through forest planning based on optimization approaches. Regardless of the owner type (state, private or common land) and/or governance model, the number of owners or management bodies considered in most studies is low, typically involving one owner/management body or a very small group. This study extends the approach of formulating a Forest Management Plan (FMP) to a large forest area, consisting of areas with different management bodies. The FMP model returns the harvest schedule that maximizes the volume of wood harvested during the planning horizon, while ensuring (1) sustainability and environmental constraints at the overall scale and (2) independent revenues for each management body. The FMP is tested in a real forested area, consisting of 22 common lands, governed by local communities for a planning period of 30 years. The results show that our approach is appropriate for several management bodies. When evaluating the impact of grouping areas (and their owner bodies) on the total volume removed, a comparison of the FMP model with an alternative model that allows for independent management (FMP-IND) showed significant differences, in terms of total volume removed at the end of the horizon. Global management leads to a reduction of about 8.6% in the total removed volume; however, it will ensure a heritage of well-diversified stands, in terms of age classes. The results highlight the importance of managing multi-stakeholder forest areas as a whole, instead of being managed independently, if the aim is to assure more sustainable management of forest resources in the mid and long term.
Responses of Early Distribution and Developmental Traits of Male and Female Trees to Stand Density in Fraxinus mandshurica Rupr. Plantation
Authors: Li Wei , Zhang Yunlong , Wei Xing , Wei Qingyu
Published: March 2022

Density plays an important role in tree growth and development. Exploring the growth of males and females in the early stage of gender differentiation and the distribution pattern in different densities are beneficial to assess the influence earlier caused by density of the productivity and reproductive potential of dioecious plantations. We observed the numbers, distribution pattern and phenotypic traits of the males and females of Fraxinus mandshurica Rupr. in four initial densities (D1: 1.5 × 3 m; D2: 2 × 2 m; D3: 1.5 × 1.5 m; D4: 1 × 1 m). The results showed that the number of males and females gradually decreased with the increase in stand density, and they were randomly distributed in each density. With the increase in density, the total volume of males and females increased first and then decreased, and the highest value appeared in the D2 (2 × 2 m) density. The phenotypic traits of males and females had no significant difference within the same density. With increasing density, the crown width and the diameter of males and females all gradually decreased. There was a larger leaf area, larger specific leaf weight, and less leaf index for males, but for females, there was a relatively stable leaf area, larger leaf biomass, and less living under branch height. In the current stage, the D2 (2 × 2 m) planting density has advantages in the number and quality of males and females. Our results emphasize that suitable stand density can promote the volume of timber accumulation and reproduction of males and females in plantations with dioecious trees.
Assessment of Three Machine Learning Techniques with Open-Access Geographic Data for Forest Fire Susceptibility Monitoring—Evidence from Southern Ecuador
Authors: Reyes-Bueno Fabián , Loján-Córdova Julia
Published: March 2022

Forest fires have become a habitual threat in all types of ecosystems, which is the reason why it is necessary to improve management of the territories and optimization of prevention and means of extinction. This study compares three machine learning techniques: logistic regression, logistic decision tree, and multivariate adaptive regression spline to identify areas susceptible to forest fires in the Loja canton. In the training of the machine learning models, a multitemporal database with 1436 points was used, fed with the information from seven variables related to fuel moisture, proximity to anthropic activities, and ground elevation. After analyzing the performance of the three models, better results were observed with the LMT, thus offering application ease for local decision-makers. The results show that the technique used allowed generating a model with a good predictive capacity and that the maps resulting from the model can be updated in short periods of time. However, it is necessary to highlight the lack meteorological data availability at the local level and to encourage future researchers to implement improvements in this regard.
Driving Forces of Forest Expansion Dynamics across the Iberian Peninsula (1987–2017): A Spatio-Temporal Transect
Authors: Padial-Iglesias Mario , Ninyerola Miquel , Serra Pere , González-Guerrero Òscar , Espelta Josep Maria , Pino Joan , Pons Xavier
Published: March 2022

This study analyzes the spatio-temporal dynamics of the drivers of forest expansion in the Iberian Peninsula for the periods 1987–2002–2017 through a 185 km-wide north–south Landsat scene transect. The analysis has considered a variety of biogeographical regions [0–3500 m.a.s.l, annual rainfalls 150–2200 mm] and 30 explanatory variables. A rigorous map production at 30 m resolution, including detailed filtering methods and uncertainty management at pixel scale, provided high-quality land cover maps. The main forest expansion trajectories were related to explanatory variables using boosted regression trees. Proximity to previous forests was a key common factor for forest encroachment in all forest types, with other factors being distance to the hydrographic network, temperature and precipitation for broadleaf deciduous forests (BDF), precipitation, temperature and solar radiation for broadleaf evergreen forests (BEF) and precipitation, distance to province capitals, and solar radiation for needleleaf evergreen forests (NEFs). Results also showed contrasting forest expansion trajectories and drivers per biogeographic region, with a high dynamism of grasslands towards new forest in the Eurosiberian and the mountainous Mediterranean regions, a high importance of croplands as land cover origin of new forest in the Mesomediterranean, and increasing importance over time of socioeconomic drivers (such as those employed in the industry sector and the utilized agricultural area) in the Supramediterranean region but the opposite pattern in the Southern Mesomediterranean. Lower precipitation rates favored new NEFs from shrublands in the Thermomediterraean region which, together with the Northern Mesomediterranean, exhibited the highest relative rates of new forests. These findings provide reliable insights to develop policies considering the ecological and social impacts of land abandonment and subsequent forest expansion.
Transient Flooding and Soil Covering Interfere with Decomposition Dynamics of Populus euphratica Leaf Litter: Changes of Mass Loss and Stoichiometry of C, N, P, and K
Authors: Yang Yuhai , Zhou Honghua , Wang Wanrui , Zhu Chenggang , Cui Dong , Ye Zhaoxia
Published: March 2022

Litter decomposition plays a critical role in carbon and nutrient cycling in terrestrial and aquatic ecosystems. However, the effects transient flooding and soil covering have on leaf litter decomposition remain unclear. The changes of litter mass loss and stoichiometric ratio of C:N (the ratio of carbon to nitrogen), C:K (the ratio of carbon to potassium), C:P (the ratio of carbon to phosphorus), N:P (the ratio of nitrogen to phosphorus), and N:K (the ratio of nitrogen to potassium) of fresh Populus euphratica (P. euphratica) leaves in surface, transient flooding, and soil covering treatments were studied using litterbags in a desert riparian forest in a field decomposition experiment for a period of 640 d. The results showed that there was a significant influence of disturbance type and incubation time on litter mass loss rate and stoichiometric ratios of C:N, C:K, C:P, N:P, and N:K of fresh P. euphratica leaves, but no significant influence of the interaction between disturbance type and incubation time on leaf litter mass loss. In three treatments, five sequential phases of leaf litter mass loss rate and different temporal change patterns of stoichiometric ratio were identified within 640 d. Transient flooding was shown to affect P. euphratica leaf litter mass loss phases compared to that in no-disturbance conditions, and especially promote leaf litter mass loss within 0–173 d of incubation time. It was also demonstrated that transient flooding and soil covering can influence leaf litter decomposition, which led to the leaf litter mass loss rate and the stoichiometric ratios of C:N, C:K, C:P, N:P, and N:K exhibiting varied patterns and phases in different treatments during decay.
Short-Term Effects of Droughts and Cold Winters on the Growth of Scots Pine at Coastal Sand Dunes around the South Baltic Sea
Authors: Janecka Karolina , Metslaid Sandra , Metslaid Marek , Harvey Jill E. , Wilmking Martin
Published: March 2022

Coastal dunes near the Baltic Sea are often stabilized by Scots pine forests and are characterized by a mild climate. These ecosystems are affected by water shortages and might be influenced by climate extremes. Considering future climate change, utilizing tree rings could help assess the role of climate extremes on coastal forest growth. We used superposed epoch analysis to study Scots pine responses to droughts and cold winters, with focus on frequency, timing, and duration. We measured ring widths (RW) and latewood blue intensity (LBI) on samples extracted from trees growing at dune ridge and bottom microsites at the south Baltic Sea. At the regional scale, we observed some similarities in tree responses to both extremes between RW and LBI within the same microsite type and region. At the local scale, RW and LBI were more frequently influenced by cold winters than droughts. RW and LBI from dune ridges were more frequently influenced by droughts than RW and LBI from dune bottoms. LBI from both microsites was more often influenced by droughts than RW. RW and LBI from both microsites were similarly often influenced by cold winters. At both scales, the response time of RW and LBI after droughts predominantly lagged by one year, while cold winters were recorded in the same year. The typical duration of growth reductions after both extremes was one year for both RW and LBI. Our study indicates that Scots pine from the Baltic Sea region is sensitive to climate extremes, especially cold winters.
New Detection Method for Fungal Infection in Silver Fir Seeds
Authors: Borowik Piotr , Stocki Marcin , Fasano Maria , Marozau Aleh , Malewski Tadeusz , Oszako Tomasz , Hsiang Tom , Tkaczyk Miłosz , Tarakowski Rafał
Published: March 2022

Silver fir trees have cycles of low and high seed production, and thus it is necessary to collect seeds in high production years to save them for low production years to ensure the continuity of nursery production. Tree seeds can be stored loosely in piles or containers, but they need to be checked for viability before planting. The objective of this study was to find a quick and inexpensive method to determine the suitability of seed lots for planting. The working hypothesis was that an electronic nose device could be used to detect odors from fungi or from decomposing organic material, and thus aid in determination of whether seeds could be sown or discarded. To affirm and supplement results from the electronic nose, we used gas chromatography–mass spectrometry (GC-MS) to detect volatile secondary metabolites such as limonene and cadienes, which were found at the highest concentrations in both, infected and uninfected seeds. Uninfected seeds contained exceptionally high concentrations of pinene, which are known to be involved in plant resistance responses. Statistically higher levels of terpineol were found in infected seeds than in uninfected seeds. A prototype of our electronic nose partially discriminated between healthy and spoiled seeds, and between green and white fungal colonies grown on incubated seeds. These preliminary observations were encouraging and we plan to develop a practical device that will be useful for forestry and horticulture.
Improved Prediction of Forest Fire Risk in Central and Northern China by a Time-Decaying Precipitation Model
Authors: Chen Jiajun , Wang Xiaoqing , Yu Ying , Yuan Xinzhe , Quan Xiangyin , Huang Haifeng
Published: March 2022

With the increase in extreme climate events, forest fires burn in much larger areas. Therefore, it is important to accurately predict forest fire frequencies. Precipitation is an important factor that affects the probability of future forest fires. Previous models used average precipitation values, but the attenuation of precipitation was not considered. In this study, a time-decaying precipitation algorithm was used to calculate the comprehensive precipitation index. This method can better represent the effect of precipitation in predicting the occurrence of forest fires. Moreover, observed fire spots were converted into a continuous density of fire spots. The structure of the prediction model is more realistic, which is conducive to obtaining higher-precision prediction results. Additionally, the support vector machine (SVM) regression model was used to construct a forest fire warning model. When the comprehensive precipitation index was compared with the average precipitation value, the accuracy of the four forest areas in central and northern China in the test set was improved by approximately 10%. The findings are relevant to forest ecologists and managers for future mitigation of forest fires, and also for successful prediction of other fire-prone areas.
Understanding the Limiting Climatic Factors on the Suitable Habitat of Chinese Alfalfa
Authors: Zhang Yanru , Liu Guan , Lu Qi , Xiong Dongyang , Li Guoqing , Du Sheng
Published: March 2022

Chinese alfalfa (Medicago sativa) is one of the most widely planted species in China. It has considerable economic potential and plays an important role in soil and water conservation. In order to conduct scientific cultivation of Chinese alfalfa, we collected 100 occurrence records from herbarium and publications and 19 climatic variables from BIOCLIM to simulate potential suitable habitat and identified the key climatic factors of Chinese alfalfa by MaxEnt and GIS software. The result shows that the MaxEnt model performed well, with an average test AUC value of 0.86 with 10-fold cross validation. The potential distribution of Chinese alfalfa is mainly in arid and semi-arid areas of north and northwest China, about 15.2% (1.46 million km2) of China’s total land area, and the highly suitable area is Loess Hilly region and Xinjiang. The main climatic factors affecting the distribution of this species is hydrological-related factors (PDM, PS, AP, PDQ and PCQ), which explained 58.6% of the variation, and the climatic factors limiting the southern, northern, northwestern and Tibetan plateau boundaries were PDM, AMT, AP and MTCM, respectively. The climatic thresholds of the core area of Chinese alfalfa are 0.0–14.0 mm of PDM, 23.8–108.2% of PS, 3.9–15.5 °C of AMT, 14.0–664.0 mm of AP, 1.0–47.0 mm of PDQ, 2.0–51.0 mm of PCQ. The results improve our understanding of limiting climatic factors for Chinese alfalfa and suggest a priority management measures for areas with corresponding limiting climatic factor.
Effects of Soil Amelioration and Vegetation Introduction on the Restoration of Abandoned Coal Mine Spoils in South Korea
Authors: Lim Bong-Soon , Kim A-Reum , Seol Jaewon , Oh Woo-Seok , An Ji-Hong , Lim Chi-Hong , Lee Chang-Seok
Published: March 2022

In order to ecologically restore coal mine spoils, tolerant species were selected through vegetation surveys on the abandoned coal mine spoils and natural forests established on the poor environment similarly to there. In addition, tolerant species were selected through cultivation experiments in the laboratory. Many C4 plants were included among the tolerant species selected through cultivation experiments. Soil was ameliorated by applying commercial organic fertilizer that can improve both physical and chemical properties of soil at the same time. Vegetation introduced for restoration was prepared by combining plant species tolerant to the degraded environment of coal mine spoils and the reference information. The treatment with a soil ameliorator improved the chemical properties of soil, such as the pH and nutrient contents, and promoted the growth of sample plants significantly. However, additional improvements were required compared with the chemical properties of healthy forest soil. The sites restored by ameliorating soil and introducing tolerant species showed a more similar species composition to the reference sites compared with the afforested and non-restored sites in both lowland and upland areas. However, such restoration did not play a significant role in increasing species diversity or excluding exotic plants. In this respect, more active restoration is recommended.
GIS-AHP Approach in Forest Logging Planning to Apply Sustainable Forest Operations
Authors: Latterini Francesco , Stefanoni Walter , Venanzi Rachele , Tocci Damiano , Picchio Rodolfo
Published: March 2022

This study represents the first attempt of integration, within a Forest Management Plan (FMP), of a Geographic Information System (GIS) and an Analytic Hierarchy Process (AHP) approach for the selection of the most suitable logging method. It is important to underline that the developed methodology is applicable worldwide in each environmental context in which there is a need for planning the intervention and selecting from among several possible logging methods or harvesting systems. Schematically, the main aims of this study were: (i) to develop a GIS-AHP method based on open-access GIS software; (ii) to compare the results of the simulations developed from the statements of two different groups of experts from around the world, to determine the reliability of the predictive probability of the method. The selection of the extraction methods performed with RTS (experts from research and technical sector) input data showed that the most suitable option in the major part of the study area was the cable skidder, followed by the cable yarder, and finally the forwarder. The extraction system selection performed with OS (people from the operative sector) input data revealed limited differences. Thus, considering what was reported above, it is possible to assert that the applied GIS-AHP methodology showed good performance and high consistency in the selection of the best alternatives among different extraction methods. The idea of comparing the results obtained from a survey based on a pool of researchers and forest engineers (RTS) was taken as a target simulation to be evaluated. The method based on data derived from a pool of expert forest operators (OS) was used to check for the results of the other simulation. This is an innovation in these kinds of studies. The results from the consistency check were encouraging, considering that for 51 sub-compartments, only two changed the selected extraction system between RTS and OS.
Within-Stem Differences in Moisture Content Loss during Transpiration and Air-Drying of Felled Oak Trees
Authors: Tomczak Arkadiusz , Tomczak Karol , Jelonek Tomasz , Naskrent Bartłomiej
Published: March 2022

This study evaluated within-stem differences in the moisture content of stored summer-harvested oak wood with respect to drying method. The felled oaks were naturally dried for eight weeks, from 4 July to 29 August 2017. We analyzed two methods of preparation and storage: a transpiration drying method (W), and an air-drying method for stem-wood (L). Transpiration drying is a better method for oak stems than air-drying. Statistically significant differences between drying methods were found after six weeks of storage. This coincided with complete wilting of the leaves. However, signs of wilting and leaf color change appeared earlier, between the second and fourth weeks of storage. In parallel, in scenario W, a statistically significant difference in MC of sapwood was observed between the second and fourth weeks of storage. Such a phenomenon was not observed in scenario L. The MC of heartwood also gradually decreased, especially in scenario W. Explanation of this phenomenon lay outside the scope of this study; however, it indicates how the structure and properties of wood, in addition to storage conditions and methods, influence the efficiency of biomass drying in the harvesting area.
Effect of Two Exogenous Organic Acids on the Excitation Effect of Soil Organic Carbon in Beijing, China
Authors: Xiao Yongli , Yu Yanni , Wang Yue , Wang Xuqin , Wang Yuanyuan , Dai Wei , Luan Yaning
Published: March 2022

Significance: The study of the effects and pathways of catechol and pyrogallic acid on soil organic carbon mineralization has a positive effect on mastering soil carbon transformation. Methods and objectives: In this study, we took 0–20 cm soil from Pinus tabulaeformis forest as an object to investigate the effects of catechol and pyrogallic acid with different concentrations on soil organic carbon mineralization through a 60-day mineralization incubation test. The soil active carbon content and changes in soil microbial diversity and community composition were analyzed by using single exponential fitting, quantitative PCR, and high-throughput sequencing to explore the influencing mechanisms of catechol and pyrogallic acid on soil organic carbon excitation. Results: Catechol and pyrogallic acid had the effect of enhancing the soil organic carbon mineralization and soil active carbon content, and the higher the concentration, the stronger the enhancement effect. Catechol reduced the Ace index, Chao1 index, and Shannon index of bacteria and fungi, and further changed the relative abundance of two dominant groups (Proteobacteria and Acidobacteriota) in bacteria and Basidiomycota in fungi at high concentrations. There was no obvious regularity in the effects of pyrogallic acid on bacteria and fungi, but the Ace index and Chao1 index of bacteria underwent drastic and disordered changes. Conclusions: Catechol and pyrogallic acid can trigger positive excitation of the soil organic carbon through two pathways: increasing the soil active carbon content and modulating soil microorganisms, but the way they modulate soil microorganisms are different. Catechol regulates soil microorganisms by reducing the number, richness, and evenness of the bacteria and fungi species, as well as the community composition, while the way pyrogallic acid regulates only closely relates to the changes in the number, richness, and evenness of bacteria species.
Alterations in Population Distribution of Liriodendron chinense (Hemsl.) Sarg. and Liriodendron tulipifera Linn. Caused by Climate Change
Authors: Cao Yiwei , Feng Jiajie , Hwarari Delight , Ahmad Baseer , Wu Haozhengji , Chen Jinhui , Yang Liming
Published: March 2022

Climate change has a significant impact on species population size and distribution, global biodiversity, and ecological status. The Liriodendron genus contains two species: Liriodendron chinense and Liriodendron tulipifera, both playing important roles in timber, medicinal, and landscape purposes. However, little is known about their population distribution characteristics and important climatic factors shaping their suitability. In this research, we used the geological record data, 19 climate components, MaxEnt, and ArcGIS to recreate and analyze the potential population distribution and their alterations of Liriodendron within the world beneath the current and future scenarios of RCP 2.6, RCP 4.5, and RCP 8.5 in 2050 and 2070. Our results showed that: Liriodendron is suitable to grow in subtropical monsoon climate areas, and that the climatic factor of precipitation of warmest quarter exerts the greatest impact on L. chinense, with a contribution rate of 57.6%. Additionally, we showed that the climatic factor of precipitation of the driest month exerts the greatest impact on L. tulipifera, with a contribution rate of 60.5%. Further analysis exhibited that low temperature and temperature fluctuations are major temperature factors affecting L. chinense and L. tulipifera, respectively. Therefore, we predicted that by the 2050s and 2070s, the areas of Liriodendron suitable habitats would increase first and then decrease in three scenarios; except the area of L. tulipifera suitable habitats under RCP8.5, which shows a slight increase. We then conclude that the Liriodendron suitable areas would shift to high latitudes due to global climate warming. The information gained from this study will provide a reference for developing forest cultivation, management, and conservation strategies for these two important tree species, and also a basis for subsequent biogeographic research.
Genetic Diversity Maximization as a Strategy for Resilient Forest Ecosystems: A Case Study on Norway Spruce
Authors: Kelblerová Radka , Dvořák Jakub , Korecký Jiří
Published: March 2022

Norway spruce, economically and ecologically one of the most important European forest tree species, rapidly declines due to massive bark beetle outbreaks across many countries. As a prerequisite of ecosystem stability facing climate changes of uncertain predictions, the reforestation management promoting locally adapted resources of broad genetic diversity should be prioritized, especially in nature conservation areas. In our case study carried out in the national park, Krkonoše Mountains (the Giant Mountains, the Czech Republic), we demonstrated a tree breeding strategy aiming at maximizing genetic diversity. More than four hundred unique Norway spruce accessions were genotyped on 15 microsatellite loci (Ne = 5.764, I = 1.713 and He = 0.685). Two core collection selection approaches were proposed to establish a new deployment population providing local gene sources of high genetic diversity. Namely, the Core Hunter selection algorithm, with average entry-to-nearest-entry distance (EN) optimization, was applied to identify the most diverse core collection set with the highest genetic diversity parameters obtained for 57 selected individuals (Ne = 6.507, I = 1.807, and He = 0.731). The latter core collection method proposed is innovative, based on choosing appropriate genotypes from a clustered heatmap. For simplicity, we demonstrated the principle of selection strategy on a reduced dataset. It is vital to promote panmixia of a newly established production population from a core collection to complete the conservation breeding effort. Thus, we demonstrated the utilization of the Optimum Neighborhood Algorithm (ONA) deployment that outperformed other deployment algorithms, especially in the case of balanced clone representation and uneven shapes of planting plots. We believe that the case study presented can be generalized and considered as a guideline for analogical tree breeding intentions.
Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis
Authors: Ong Seow-Chin , Cheng Wei-Hung , Ku Fu-Man , Tsai Chih-Yu , Huang Po-Jung , Lee Chi-Ching , Yeh Yuan-Ming , Rada Petr , Hrdý Ivan , Narayanasamy Ravi Kumar , Smutná Tamara , Lin Rose , Luo Hong-Wei , Chiu Cheng-Hsun , Tachezy Jan , Tang Petrus
Published: March 2022

Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal epithelial cells and animal models. These results prompted us to examine whether EVs released from TVV+ isolates contained TVV. We isolated small extracellular vesicles (sEVs) from six T. vaginalis isolates that were either TVV free (ATCC 50143), harbored a single (ATCC 30236, ATCC 30238, T1), two (ATCC PRA-98), or three TVV subspecies (ATCC 50148). The presence of TVV subspecies in the six isolates was observed using reverse transcription-polymerase chain reaction (RT-PCR). Transmission electron microscopy (TEM) confirmed the presence of cup-shaped sEVs with a size range from 30–150 nm. Trichomonas vaginalis tetraspanin (TvTSP1; TVAG_019180), the classical exosome marker, was identified in all the sEV preparations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that all the sEVs isolated from TVV+ isolates contain viral capsid proteins derived from the same TVV subspecies in that isolate as demonstrated by RT-PCR. To provide more comprehensive information on the TVV subspecies population in other T. vaginalis isolates, we investigated the distribution of TVV subspecies in twenty-four isolates by mining the New-Generation Sequencing (NGS) RNAseq datasets. Our results should be beneficial for future studies investigating the role of TVV on the pathogenicity of T. vaginalis and the possible transmission of virus subspecies among different isolates via sEVs.
Are Roma People Descended from the Punjab Region of Pakistan: A Y-Chromosomal Perspective
Authors: Adnan Atif , Rakha Allah , Lazim Hayder , Nazir Shahid , Al-Qahtani Wedad Saeed , Abdullah Alwaili Maha , Hadi Sibte , Wang Chuan-Chao
Published: March 2022

Gypsies are a separate ethnic group living in Pakistan and some other countries as well. They are mostly known as ‘Roma’ and ‘untouchables’. They have different types of lifestyles as compared to other common people, as they always keep migrating from one place to another. They do not have proper houses; they live in tent houses and most probably work on daily wages to earn their living. Gypsies cannot be specified according to the place of residence and can only be classified according to their migration route. Previous historical and linguistic research showed the north Indian origin of Roma people. The present study collected 285 unrelated Roma individuals living in Punjab and typed with the Goldeneye Y20 system. Allelic frequencies ranged between 0.0035 and 0.5266, with haplotype diversity (HD) of 0.9999 and discrimination capacity (DC) of 0.8790. Gene diversity (GD) ranged from 0.6489 (DYS391) to 0.9764 (DYS391) (DY385ab). A total of 223 unique alleles were observed. Interestingly, the haplogroup R accounted for 40.56% and J for 22.06%. In MDS analysis, Pakistani Roma formed a close cluster with Roma from Constanta, Romania. The migration pattern of the Roma population from Pakistan, India and Europe was inferred using coalescence theory in the Migrate-n program. Overlapping Y-STR data were used to test different migration models. These migration models showed us the dominant gene flow from Pakistan to India and Europe to Pakistan. The results of our study showed that Y STRs provided substantially stronger discriminatory power in the Pakistani Roma population.
Transcriptomics of Wet Skin Biopsies Predict Early Radiation-Induced Hematological Damage in a Mouse Model
Authors: Alkhalil Abdulnaser , Clifford John , Miller Stacy Ann , Gautam Aarti , Jett Marti , Hammamieh Rasha , Moffatt Lauren T. , Shupp Jeffrey W.
Published: March 2022

The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using wet skin (blood/skin) biopsies obtained at hour 2 and days 4, 7, 21, and 28 from a mouse radiation model. Analysis of significantly differentially transcribed genes (SDTG; p ≤ 0.05 and FC ≥ 2) during the first post-exposure week identified the glycoprotein 6 (GP-VI) signaling, the dendritic cell maturation, and the intrinsic prothrombin activation pathways as the top modulated pathways with stable inactivation after lethal exposures (20 Gy) and intermittent activation after sublethal (1, 3, 6 Gy) exposure time points (TPs). Interestingly, these pathways were inactivated in the late TPs after sublethal exposure in concordance with a delayed deleterious effect. Modulated transcription of a variety of collagen types, laminin, and peptidase genes underlay the modulated functions of these hematologically important pathways. Several other SDTGs related to platelet and leukocyte development and functions were identified. These results outlined genetic determinants that were crucial to clinically documented radiation-induced hematological and skin damage with potential countermeasure applications.
Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches
Authors: D’Esposito Rebecca J. , Myers Christopher A. , Chen Alan A. , Vangaveti Sweta
Published: March 2022

RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.
Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Alliumcepa L.)
Authors: Lee Hyun-Min , Park Jee-Soo , Kim So-Jeong , Kim Seung-Gyu , Park Young-Doo
Published: March 2022

Gray mold disease caused by Botrytis in onions (Allium cepa L.) during growth and storage negatively affects their yield and quality. Exploring the genes related to gray mold resistance in onion and their application to the breeding of resistant onion lines will support effective and ecological control methods of the disease. Here, the genetic relationship of 54 onion lines based on random amplified polymorphic DNA (RAPD) and in vitro-cultured onion lines infected with gray mold were used for screening resistance and susceptibility traits. Two genetically related onion lines were selected, one with a resistant and one with a susceptible phenotype. In vitro gray mold infection was repeated with these two lines, and leaf samples were collected for gene expression studies in time series. Transcript sequences obtained by RNA sequencing were subjected to DEG analysis, variant analysis, and KEGG mapping. Among the KEGG pathways, ‘α-linoleic acid metabolism’ was selected because the comparison of the time series expression pattern of Jasmonate resistant 1 (JAR1), Coronatine-insensitive protein 1 (COI 1), and transcription factor MYC2 (MYC2) genes between the resistant and susceptible lines revealed its significant relationship with gray-mold-resistant phenotypes. Expression pattern and SNP of the selected genes were verified by quantitative real-time PCR and high-resolution melting (HRM) analysis, respectively. The results of this study will be useful for the development of molecular marker and finally breeding of gray-mold-resistant onions.
Identification of Frameshift Variants in POLH Gene Causing Xeroderma Pigmentosum in Two Consanguineous Pakistani Families
Authors: Zamani Ghazala Y. , Khan Ranjha , Karim Noreen , Ahmed Zubair M. , Naeem Muhammad
Published: March 2022

Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder characterized by severe sensitivity of skin to sunlight and an increased risk of skin cancer. XP variant (XPV), a milder subtype, is caused by variants in the POLH gene. POLH encodes an error-prone DNA-polymerase eta (pol eta) which performs translesion synthesis past ultraviolet photoproducts. The current study documents the clinical and genetic investigations of two large consanguineous Pakistani families affected with XPV. In family 1, whole exome sequencing (WES) revealed a novel frameshift variant, c.1723dupG (p.(Val575Glyfs*4)), of POLH, which is predicted to cause frameshift and premature truncation of the encoded enzyme. Indeed, our ex vivo studies in HEK293T cells confirmed the truncation of the encoded protein due to the c.1723dupG variant. In family 2, Sanger sequencing of POLH exons, revealed a recurrent nonsense variant, c.437dupA (p.Tyr146*). POLH forms a hetero-tetrameric POLZ complex with REV3L, REV7, POLD2 and POLD3. Next, we performed in silico analysis of POLH and other POLZ complex genes expression in publicly available single cell mRNAseq datasets from adult human healthy and aging skin. We found overlapping expression of POLH, REV3L and POLD2 in multiple cell types including differentiated and undifferentiated keratinocytes, pericytes and melanocytes in healthy skin. However, in aging human skin, POLH expression is reduced in compare to its POLZ complex partners. Insights from our study will facilitate counseling regarding the molecular and phenotypic landscape of POLH-related XPV.
Preferentially Expressed Antigen in Melanoma (PRAME) and Human Malignant Melanoma: A Retrospective Study
Authors: Cazzato Gerardo , Mangialardi Katia , Falcicchio Giovanni , Colagrande Anna , Ingravallo Giuseppe , Arezzo Francesca , Giliberti Giovanna , Trilli Irma , Loizzi Vera , Lettini Teresa , Scarcella Sara , Annese Tiziana , Parente Paola , Lupo Carmelo , Casatta Nadia , Maiorano Eugenio , Cormio Gennaro , Resta Leonardo , Ribatti Domenico
Published: March 2022

Background: Preferentially expressed antigen in melanoma (PRAME) is a cancer testis antigen (CTA) identified in 1997 through analysis of the specificity of tumor-reactive T-cell clones derived from a patient with metastatic cutaneous melanoma. Although at first it seemed even more specific, various studies have shown that PRAME can also be expressed in the context of atypical lesions that do not correspond solely to the definition of malignant melanoma. Methods: A systematic review of English articles was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: 126 records were identified in the literature search, of which 9 were duplicates. After screening for eligibility and inclusion criteria, 53 publications were included. Conclusions: The advent of a new marker such as PRAME is surely a step forward not only in the diagnostic approach, but also in the immunotherapeutic approach to MM. However, various studies have shown that PRAME can also be expressed in the context of atypical lesions apart from MM and, for this reason, the diagnostic sensitivity and specificity (hence accuracy) are clearly lower. Further studies with larger case series will be necessary to understand better what possibilities are offered in terms of diagnostic reliability by PRAME.
Gnas Promoter Hypermethylation in the Basolateral Amygdala Regulates Reconsolidation of Morphine Reward Memory in Rats
Authors: Liu Peng , Liang Jialong , Jiang Fengze , Cai Wanshi , Shen Fang , Liang Jing , Zhang Jianjun , Sun Zhongsheng , Sui Nan
Published: March 2022

Impairing reconsolidation may disrupt drug memories to prevent relapse, meanwhile long-term transcription regulations in the brain regions contribute to the occurrence of emotional memories. The basolateral amygdala (BLA) is involved in the drug-cue association, while the nucleus accumbens (NAc) responds to the drug reward. Here, we assessed whether DNA methyltransferases (Dnmts) in these two brain regions function identically in the reconsolidation of morphine reward memory. We show that Dnmts inhibition in the BLA but not in the NAc after memory retrieval impaired reconsolidation of a morphine reward memory. Moreover, the mRNA levels of Dnmt3a and Dnmt3b, rather than Dnmt1, in the BLA were continuously upregulated after retrieval. We further identified the differentially methylated regions (DMRs) in genes in the BLA after retrieval, and focused on the DMRs located in gene promoter regions. Among them were three genes (Gnas, Sox10, and Pik3r1) involved in memory modulation. Furthermore, Gnas promoter hypermethylation was confirmed to be inversely correlated with the downregulation of Gnas mRNA levels. The findings indicate that the specific transcription regulation mechanism in the BLA and NAc on reconsolidation of opiate-associated memories can be dissociable, and DNA hypermethylation of Gnas in the BLA is necessary for the reconsolidation of morphine reward memories.
Note on DNA Analysis and Redesigning Using Markov Chain
Authors: Zakarczemny Maciej , Zajęcka Małgorzata
Published: March 2022

The paper contains a discussion on mathematical modifying and redesigning DNA with the use of Markov chains. We give a simple mathematical technique for overwriting missing parts of DNA. With a certain probability (without even knowing the function of the missing codon) we can find a synonymous codon, so that there is no frequency change in amino acid sequences of proteins. We use Markov Chain to analyze the dependencies in DNA sequence of the human gene Alpha 1,3-Galactosyltransfe rase 2. We include a theoretical introduction which facilitates the understanding of the paper for non-mathematicians, especially for biologists not familiar with the theory of Markov chains.
National Genome Initiatives in Europe and the United Kingdom in the Era of Whole-Genome Sequencing: A Comprehensive Review
Authors: Smetana Jan , Brož Petr
Published: March 2022

Identification of genomic variability in population plays an important role in the clinical diagnostics of human genetic diseases. Thanks to rapid technological development in the field of massive parallel sequencing technologies, also known as next-generation sequencing (NGS), complex genomic analyses are now easier and cheaper than ever before, which consequently leads to more effective utilization of these techniques in clinical practice. However, interpretation of data from NGS is still challenging due to several issues caused by natural variability of DNA sequences in human populations. Therefore, development and realization of projects focused on description of genetic variability of local population (often called “national or digital genome”) with a NGS technique is one of the best approaches to address this problem. The next step of the process is to share such data via publicly available databases. Such databases are important for the interpretation of variants with unknown significance or (likely) pathogenic variants in rare diseases or cancer or generally for identification of pathological variants in a patient’s genome. In this paper, we have compiled an overview of published results of local genome sequencing projects from United Kingdom and Europe together with future plans and perspectives for newly announced ones.