Biologia futuraPub Date : 2023-12-01Epub Date: 2024-02-01DOI: 10.1007/s42977-024-00201-x
Emese Meglécz
{"title":"mkLTG: a command-line tool for taxonomic assignment of metabarcoding sequences using variable identity thresholds.","authors":"Emese Meglécz","doi":"10.1007/s42977-024-00201-x","DOIUrl":"10.1007/s42977-024-00201-x","url":null,"abstract":"<p><p>Metabarcoding is now a widely used method for biodiversity studies. Taxonomic assignment of environmental sequences is one of the key steps of metabarcoding. Assignments based on lowest common ancestor (LCA) method generally rely on fixed arbitrary thresholds, and this is generally not well adapted for assignment of taxonomically diverse groups with variable coverage in reference databases. The mkLTG is a LCA-based method that uses a series of percentage of identity thresholds starting from stringent parameters and decreasing it if necessary. All parameters can be set separately for each percentage of identity threshold, which makes this tool adaptable for different databases, genetic markers and diverse taxonomic groups. The optimization step was included using the COI marker and a comprehensive, non-redundant database. The mkLTG tool is a command-line application with few dependencies that runs in all operating systems, therefore, it is easy to include into complex pipelines. All scripts are freely available including the benchmarking at https://github.com/meglecz/mkLTG .</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"369-375"},"PeriodicalIF":1.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-12-01Epub Date: 2024-03-11DOI: 10.1007/s42977-024-00211-9
Katalin Pecsenye, Judit Bereczki, Amáta Hollós, Zoltán Varga
{"title":"Evolutionary significant units (ESUs) and functional conservation units (FCUs) in the Phengaris (Maculinea) nausithous populations of East-Central Europe.","authors":"Katalin Pecsenye, Judit Bereczki, Amáta Hollós, Zoltán Varga","doi":"10.1007/s42977-024-00211-9","DOIUrl":"10.1007/s42977-024-00211-9","url":null,"abstract":"<p><p>The aim of this study was to analyse the level and structure of genetic and morphometric variation in the East-Central European populations of Phengaris (Maculinea) nausithous. On the basis of the life cycle of the species, we expected a low level of variation within the populations coupled with a relatively high level of differentiation among them. We also assumed that the differentiation among the populations has a regional pattern. In order to confirm these assumptions, we collected population samples from two regions within the Carpathian Basin (western Transdanubia and Transylvania) and from a region east of the Carpathian Mountains (Bukovina). The level of enzyme polymorphism and the amount of morphometric variation were investigated in the sampled populations. As the western (Transdanubia) and the eastern populations (Transylvania plus Bukovina) were suggested to belong to different subspecies (Rákosy et al. in Nota Lepidopterol 33:31-37, 2010), our working hypothesis was that these two groups of populations belong to different evolutionary significant units (ESUs). The results of all genetic analyses (PCA, Bayesian-clustering analysis and especially the UPGMA dendrogram) confirmed our assumption. The level of differentiation was higher between the western and eastern populations resulting in two monophyletic lineages of Phengaris (Maculinea) nausithous in East-Central Europe. This result suggests that these lineages can be considered as two different ESUs.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"445-455"},"PeriodicalIF":1.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140100986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-09-01Epub Date: 2023-10-18DOI: 10.1007/s42977-023-00185-0
Vera Gál, Zsuzsanna Dömötör
{"title":"The role of connection with nature in empirical studies with physiological measurements: a systematic literature review.","authors":"Vera Gál, Zsuzsanna Dömötör","doi":"10.1007/s42977-023-00185-0","DOIUrl":"10.1007/s42977-023-00185-0","url":null,"abstract":"<p><p>It is well described that exposure to nature reduces physiological stress, and connectedness to nature can have a moderating effect. However, few studies have so far examined the construction of the connection with nature in relation to physiological processes. In this systematic review, we collected studies that used a physiological measure and included a scale to measure connectedness to nature. Our aim was to assess the role of nature relatedness at the level of physiological processes and to summarize the results published so far. Our review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. A literature search was conducted in 3 different databases (PubMed, ScienceDirect and Google Scholar). As keywords, we used all the different questionnaires that measure connectedness to nature, combined with terms related to physiological measures. After final screening, 28 articles met the inclusion criteria for the review. The studies were very diverse in terms of purpose, intervention and methods, so narrative synthesis was conducted without measures of effect. We found evidence for a mediating effect of nature connectedness on the associations between nature exposure and cognitive function, brain activity, blood pressure, cortisol level and mental health. Studies investigating nature relatedness as state-like characteristics have shown that exposure to nature increases the level of connection to nature. Eye-tracking studies have confirmed that this measurement method can be used to investigate nature relatedness at a physiological level, which could be a useful complement to self-report questionnaires in future studies.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"281-294"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41232009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-09-01Epub Date: 2023-10-09DOI: 10.1007/s42977-023-00178-z
Beáta Korcsok, Péter Korondi
{"title":"How do you do the things that you do? Ethological approach to the description of robot behaviour.","authors":"Beáta Korcsok, Péter Korondi","doi":"10.1007/s42977-023-00178-z","DOIUrl":"10.1007/s42977-023-00178-z","url":null,"abstract":"<p><p>The detailed description of behaviour of the interacting parties is becoming more and more important in human-robot interaction (HRI), especially in social robotics (SR). With the rise in the number of publications, there is a substantial need for the objective and comprehensive description of implemented robot behaviours to ensure comparability and reproducibility of the studies. Ethograms and the meticulous analysis of behaviour was introduced long ago in animal behaviour research (cf. ethology). The adoption of this method in SR and HRI can ensure the desired clarity over robot behaviours, while also providing added benefits during robot development, behaviour modelling and analysis of HRI experiments. We provide an overview of the possible uses and advantages of ethograms in HRI, and propose a general framework for describing behaviour which can be adapted to the requirements of specific studies.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"253-279"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41124046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-09-01Epub Date: 2023-09-27DOI: 10.1007/s42977-023-00182-3
A Rácz, Gy Czégény, D Kutyáncsánin, N Nagy, É Hideg, K Csepregi
{"title":"Fight against cold: photosynthetic and antioxidant responses of different bell pepper cultivars (Capsicum annuum L.) to cold stress.","authors":"A Rácz, Gy Czégény, D Kutyáncsánin, N Nagy, É Hideg, K Csepregi","doi":"10.1007/s42977-023-00182-3","DOIUrl":"10.1007/s42977-023-00182-3","url":null,"abstract":"<p><p>The special metabolites of bell pepper (Capsicum annuum L.) leaves can protect the plant under possibly damaging circumstances, such as high light, UV, unfavorable temperatures, or other environmental effects. In this study, we examined the cold stress tolerance of three different Hungarian pepper varieties (Darina, Édesalma, Rekord), focusing on the antioxidant and photosynthetic responses. The plants were developed in growth chambers under optimal temperature conditions (day/night 25 °C/20 °C) until the leaves on the fourth node became fully developed, then half of the plants received a cold treatment (day/night 15 °C/10 °C). Via a detailed pigment analysis, the PS II chlorophyll fluorescence responses, gas exchange parameters and total antioxidant capacities, leaf acclimation to low temperatures has been characterized. Our results display some of the developing physiological and antioxidant properties, which are among the main factors in monitoring the damaging effects of cold temperatures. Nevertheless, despite their differences, the tested pepper varieties did not show different cold responses.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"327-335"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41100909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-09-01Epub Date: 2023-10-09DOI: 10.1007/s42977-023-00184-1
Bernadett Bákány, Réka Antal, Péter Szentesi, Tamás Emri, Éva Leiter, László Csernoch, Nancy P Keller, István Pócsi, Beatrix Dienes
{"title":"The bZIP-type transcription factors NapA and RsmA modulate the volumetric ratio and the relative superoxide ratio of mitochondria in Aspergillus nidulans.","authors":"Bernadett Bákány, Réka Antal, Péter Szentesi, Tamás Emri, Éva Leiter, László Csernoch, Nancy P Keller, István Pócsi, Beatrix Dienes","doi":"10.1007/s42977-023-00184-1","DOIUrl":"10.1007/s42977-023-00184-1","url":null,"abstract":"<p><p>Basic leucine zipper (bZIP) transcription factors are crucial components of differentiation, cellular homeostasis and the environmental stress defense of eukaryotes. In this work, we further studied the consequence of gene deletion and overexpression of two bZIP transcription factors, NapA and RsmA, on superoxide production, mitochondrial morphology and hyphal diameter of Aspergillus nidulans. We have found that reactive oxygen species production was influenced by both gene deletion and overexpression of napA under tert-butylhydroperoxide (tBOOH) elicited oxidative stress. Furthermore, gene expression of napA negatively correlated with mitochondrial volumetric ratio as well as sterigmatocystin production of A. nidulans. High rsmA expression was accompanied with elevated relative superoxide ratio in the second hyphal compartment. A negative correlation between the expression of rsmA and catalase enzyme activity or mitochondrial volumetric ratio was also confirmed by statistical analysis. Hyphal diameter was independent on either rsmA and napA expression as well as 0.2 mM tBOOH treatment.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"337-346"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41181983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-09-01Epub Date: 2023-07-26DOI: 10.1007/s42977-023-00174-3
Alexander V Sirotkin
{"title":"Peppers and their constituents against obesity.","authors":"Alexander V Sirotkin","doi":"10.1007/s42977-023-00174-3","DOIUrl":"10.1007/s42977-023-00174-3","url":null,"abstract":"<p><p>Phytotherapy can be an efficient tool for prevention and treatment of disorders including obesity. The purpose of this narrative review is to summarize the available knowledge concerning the positive effects of peppers (Capsicum spp.) and their alkaloid capsaicin on human health, in particular on fat and obesity. Search for literature was performed in Medline/Pubmed, Web of Science and SCOPUS databases between the year 2000 and 2023. Words used to search were pepper, Capsicum, capsaicin, review, obesity, fat, weight loss and mechanisms. The available data demonstrate that both pepper extract and capsaicin can positively influence human health and treat several disorders. Moreover, they can reduce fat storage affecting brain centres responsible for the sensation of hunger, nutrient uptake by gastrointestinal tract, state of adipocytes, increase in carbohydrate and fat oxidation, metabolism and thermogenesis and other mechanisms. Therefore, despite some possible limitations, these substances could be useful for treatment of obesity.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"247-252"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10248351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses.","authors":"Dima Faris Abdulkhadum Al-Mamoorı, Yasemin Celik Altunoglu, Erdoğan Horuz, Büşra Özkan Kök","doi":"10.1007/s42977-023-00176-1","DOIUrl":"10.1007/s42977-023-00176-1","url":null,"abstract":"<p><p>Sugar beet (Beta vulgaris ssp. vulgaris) is primarily used in sugar production worldwide. Expansins are a gene family of cell wall proteins effective in regulating cell wall structure. They also participate in developmental stages, including cell and leaf growth, root development, and fruit ripening. This study comprehensively characterizes the expansin gene family members found in the sugar beet genome. In addition, in silico expression analysis of sugar beet expansin genes under variable abiotic stress conditions and expression profiles of expansin genes under combined drought and heat stresses by the qRT-PCR method were evaluated in the study. A total of 31 sugar beet expansin genes were identified. BvuEXLA-02 and BvuEXLB-02 genes can have abiotic stress tolerance roles besides their roles in normal development. Determining the properties of sugar beet expansin, family members can help enable the cellulose hydrolysis mechanism and raise plant biomass. Elucidating expression profiles of the sugar beet expansin genes under variable stress conditions can support improving plant productivity. The results of the current study may also contribute to the deep understanding of sugar beet expansin genes in the future.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"295-307"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10467722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-09-01Epub Date: 2023-09-21DOI: 10.1007/s42977-023-00179-y
Sarita Sharma, Meenu Saraf
{"title":"Biofilm-forming plant growth-promoting rhizobacterial consortia isolated from mines and dumpsites assist green remediation of toxic metal (Ni and Pb) using Brassica juncea.","authors":"Sarita Sharma, Meenu Saraf","doi":"10.1007/s42977-023-00179-y","DOIUrl":"10.1007/s42977-023-00179-y","url":null,"abstract":"<p><p>To study how biofilm-forming rhizobacteria isolated from mines and dumpsites improved the phytoremediation efficacy of B. juncea in metal-contaminated soil. Out of 91 isolates, six were chosen for research based on their tolerance to metals, and their efficient PGPR properties, and subjected to the design of a consortium. A compatibility study revealed no antagonistic interaction between rhizobacterial-consortiums. The results of the biofilm formation and FEG-SEM studies revealed that a consortium-BC8 formed a strong biofilm on the root surface of B. juncea seedlings. Based on results obtained with the phytoextraction efficiency of B. juncea in consortium-BC8 (SMHMZ46 and SMHMP23), they were identified as Klebsiella variicola and Pseudomonas otitidis, respectively, and submitted to NCBI GenBank with accession numbers MZ145092 and OK560623. This rhizobacteria is the first to be reported as assisting Ni and Pb phytoremediation by employing B. juncea. Soil inoculation with consortium-BC8 increased the amount of soluble Ni and Pb by 13.25-fold and 10.69-fold, respectively, when compared to the control. These consortiums-BC8 significantly increased vegetative growth and metal accumulation in root and shoot with a translocation-factor of 1.58 for Ni and soil to root with a bioconcentration-factor of 1.3 for Pb in B. juncea grown in individual soil contamination with 96.05 mg/kg NiCl<sub>2</sub> and 89.63 mg/kg Pb(NO<sub>3</sub>)<sub>2</sub>, which are significantly higher than other consortium treatments and the non-inoculated control. B. juncea amendments with a biofilm-forming consortium-BC8 having TF, BCF, and BAC > 1 for Ni, whereas BCF > 1, TF, and BAC < 1 for Pb, are appropriate for green remediation of Ni and phytostabilization of Pb.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":" ","pages":"309-325"},"PeriodicalIF":2.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41099436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biologia futuraPub Date : 2023-06-01DOI: 10.1007/s42977-023-00153-8
Ernő Duda
{"title":"How much (evil) intelligence can be encoded by 30 kb?","authors":"Ernő Duda","doi":"10.1007/s42977-023-00153-8","DOIUrl":"https://doi.org/10.1007/s42977-023-00153-8","url":null,"abstract":"<p><p>Genomes of most RNA viruses are rarely larger than the size of an average human gene (10-15 kb) and still code for a number of biologically active polypeptides that modify the immune system and metabolism of the host organism in an amazingly complex way. Prolonged coevolution developed tricks by which viruses can dodge many protective mechanisms of the host and lead to the formation of molecular mimicry patterns. Some viruses inhibit the interferon response, interfere with the membrane destroying effects of the activated complement cascade. They can replicate in cellular compartments formed by inner membranes of the cell hiding their characteristic features from diverse pattern recognition receptors. In many cases-and in this respect, the new coronavirus is a champion-they can exploit our own defensive mechanisms to cause serious harm, severe symptoms and frequently deadly disease.</p>","PeriodicalId":8853,"journal":{"name":"Biologia futura","volume":"74 1-2","pages":"61-67"},"PeriodicalIF":2.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9907195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9884670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}