Low Level Of Similarity Research Articles

Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex

Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2–4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.

The First Pseudomonas Phage vB_PseuGesM_254 Active against Proteolytic Pseudomonas gessardii Strains

Bacteria of the Pseudomonas genus, including the Pseudomonas gessardii subgroup, play an important role in the environmental microbial communities. Psychrotolerant isolates of P. gessardii can produce thermostable proteases and lipases. When contaminating refrigerated raw milk, these bacteria spoil it by producing enzymes resistant to pasteurization. One possible way to prevent spoilage of raw milk is to use Pseudomonas lytic phages specific to undesirable P. gessardii isolates. The first phage, Pseudomonas vB_PseuGesM_254, was isolated and characterized, which is active against several proteolytic P. gessardii strains. This lytic myophage can infect and lyse its host strain at 24 °C and at low temperature (8 °C); so, it has the potential to prevent contamination of raw milk. The vB_PseuGesM_254 genome, 95,072 bp, shows a low level of intergenomic similarity with the genomes of known phages. Comparative proteomic ViPTree analysis indicated that vB_PseuGesM_254 is associated with a large group of Pseudomonas phages that are members of the Skurskavirinae and Gorskivirinae subfamilies and the Nankokuvirus genus. The alignment constructed using ViPTree shows that the vB_PseuGesM_254 genome has a large inversion between ~53,100 and ~70,700 bp, which is possibly a distinctive feature of a new taxonomic unit within this large group of Pseudomonas phages.

Tracing the Linguistic Roots of Malay and Batak Languages in Sumatra Island: A Historical Comparative Study

Previous research in comparative historical linguistics has traditionally focused on languages within a single region, overlooking cognate languages in other areas. This study seeks to rectify this by quantitatively and qualitatively describing the kinship between Rejang, Serawai, Lembak (Bengkulu), and Toba, Mandailing, and Nias (North Sumatra) languages. It aims to unearth empirical evidence regarding the timing of divergence between Malay and Batak languages, as well as the grouping of languages and the percentage of kinship between Bengkulu Province and North Sumatra Province. Utilizing Morris Swadesh's lexicostatistics and glottochronology methods, the research evaluates word kinship based on a fundamental 150-word list. Results indicate significant differences among the six languages, particularly with Rejang and Nias displaying low similarity levels, falling below 30% and not even reaching 10%, respectively. The percentage of kinship between local language pairs in Bengkulu and North Sumatra Province averages at 22.66%, classifying them under the "Family stock" category, indicating identical word correlations despite differing phonetic elements. Glottochronological calculations estimate the separation time between Malay and Batak languages to range from 419 to 3,289 BC. This research significantly enhances understanding of regional language kinship and linguistic diversity.

Keragaman Pepaya (Carica papaya L.) di Kotamadya Pontianak Berdasarkan Karakter Morfologi

Papaya (Carica papaya L.) is a plant that is widely cultivated in Indonesia. Pontianak City is one of the centers for the production of papaya cultivation, with a production of 12,593 tons in 2019. This study aims to determine the diversity and kinship of papaya in Pontianak City based on its morphological characters. The research was conducted from September to October 2021 in Pontianak City. A total of 32 individuals were sampled from six districts using the cruising method. Consanguinity was analyzed on 28 morphological characters using the UPGMA method with the NTSYS ver. 2.0. The results indicated that the 32 papaya accessions exhibited a similarity coefficient value of 0.35, which represents a 35% level of similarity. The papaya plants in Pontianak City exhibited a low level of similarity but a high level of diversity.

Evidence from temperature analog for traditional and economic cities in Nigeria: implications for sustainable city-related actions

Responding to the threats of climate change by cities requires taking relevant actions that will communicate future conditions in reliable and effective manner for sustainable and transformational climate actions. We used the analog approach to assess the geographical shifts and changes in average temperature conditions for six traditional and economic cities under different climate scenarios (Mitigated and Unmitigated scenarios). We calculated the similarity in temperature between each pixel for the current (2021–2050) and future (2041–2070) conditions of the cities, with every pixel globally in the historical (1971–200) period. Our analysis revealed that; (1) the temperature of the cities in the current and future periods will be similar to conditions of another place on the globe during the historical period; (2) Kano city will experience even more drastic changes because of the low level of similarity to other places; (3) the new places found with similar temperature conditions are generally to the south of the corresponding cities thus indicating warming. The overall results show that the analogues of the cities are within the domain of the global tropical zone which occurs around the equator. Drawing from the interaction between cities and their analogues, we highlighted sustainable city related actions such as the incorporation of urban designs and policies to enhance human thermal comfort as adaptation and solution strategies. While future research might apply qualitative studies and additional data to support the analog results, our findings can guide the understanding and application of the analog approach into environmental issues in Nigeria and other West African countries in accordance to sustainable city goals (SDG 11).

Editorial

Editorial

IMPLEMENTATION OF IMAGE ANALYSIS FROM THIN LAYER CHROMATOGRAM OF PURPLE SWEET POTATO LEAF EXTRACT IN CHEMICAL FINGERPRINTING

Background: Purple sweet potato (Ipomoea batatas L.) is a crop that contains rich amounts of anthocyanins and flavonoids. For maintaining its quality in preparations, fingerprint analysis using Thin Layer Chromatography (TLC) is commonly used. Objective: In this study, image analysis was implemented on the chromatogram to develop fingerprint profiles of the leaves of various types of purple sweet potatoes. Methods: Fingerprint analysis and acquisition of data were carried out by combining modern TLC equipment with software for image analysis. The in-situ fingerprint analysis using WinCats was compared with the image analysis results obtained in this study. The chemometric technique, cluster analysis, was performed to measure their difference in terms of sample classification. Cluster analysis was carried out to confirm that the clusters formed from image analysis were the same as those from WinCats. Results: The results obtained were two dendrograms, both showing the formation of two clusters but with a different order of samples. This study concluded that the data obtained from image analysis using ImageJ software resulted in clustering with a similarity of 38.15%, while the data obtained from WinCats software resulted in classification with a similarity of 28.31%. Both methods had issues in determining the fingerprint profiles, as evidenced by the low level of similarity. Conclusion: These results indicate that image analysis has the potential to be implemented for fingerprint profile development. However, further analysis is needed to align the Rf values and confirm the compounds in the peaks.

Utilization of Fuzzy Ontology for the Meaning of Homonymous and Homophones Ambiguous Sentences

The ambiguous sentences Homonyms and Homophones become a big problem when processed by computers. From these problems, a Novelty was found; the Novelty created a system that was able to recognize ambiguous sentences of Homonyms and Homophones. The process that the system runs for the first time is to test the proximity of the ambiguous sentences entered with the data set; from this process, the ambiguous sentences entered can already be recognized as the meaning of the sentence. The resulting result is how many per cent the level of similarity. Then the results are processed with the fuzzy ontology method. The results of the Fuzzy Ontology are low similarity level, moderate similarity level, and high similarity level. The method used to analyze this research is the confusion matrix, the precision results obtained were 92%, recall was 100%, and accuracy was 96%. In the future, this research can be used to refine translation results in a translation system.

Diversity, distribution patterns and indicatory potential of echinoderm communities of the tropical East Atlantic (Gulf of Guinea): Influence of multiple natural and anthropogenic factors along a 25–1000 m depth gradient

All earlier studies of the West African echinoderm fauna have focused on taxonomy, and general knowledge about benthic community responses to various human related threats are poorly diagnosed and not monitored along the whole African coast. Our analysis of diversity and distribution patterns of Ghanaian echinoderms yielded 36 species. Material was collected at nine transects distributed along the coast of Ghana (25–1000 m depth range, total of over 270 samples). Gradual decreases in species richness, diversity, evenness and abundance were observed along the depth gradient, with the most diverse fauna being recorded on the shelf (25–50 m). The most abundant species were Ophiactis luetkeni and Ophiothrix congensis, although both had very patchy distributions. Cluster analysis separated shelf communities (25–100 m) from slope communities (500–1000 m), although on a low level of similarity. Our analysis allowed to select most vulnerable benthic habitats that should be amongst priorities of the future monitoring. Local influence of arsenic was observed at some shelf sites, while slope fauna was affected by elevated levels of hydrocarbons and barium. Changes in salinity and fluorescence also influenced echinoderm assemblages. The most general trend showed patchily distributed, diverse shallow water fauna being influenced by increased microhabitat diversity and food availability, while depauperate slope fauna was affected by local disturbances associated with oil extraction. Tropical echinoderm communities have a great potential as indicators of even minor and local pollution, although high patchiness and low abundance creates difficulties in the multivariate analysis. High sampling effort and high number of replicates allowed to minimise those problems and demonstrated small scale microhabitat diversity.

Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea.

Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.

Genetic diversity and its association with Phytophthora palmivora resistance in Durian (Durio zibethinus) using RAPD markers

Abstract. Numba S. 2023. Genetic diversity and its association with Phytophthora palmivora resistance in Durian (Durio zibethinus) using RAPD markers. Biodiversitas 24: 4542-4548. Durian (Durio zibethinus L.) is a popular tropical fruit that contributes significantly to regional economic value. Root and stem rot disease caused by Phytophthora palmivora has become a serious threat to the growth and development of durian. Indonesia has various local durian varieties that have the potential of resistant to P. palmivora. This study aims to analyze genetic diversity and its association with the resistance of durian to root and stem rot disease caused by P. palmivora using RAPD markers. Ten varieties of durian were compared with those of 2 wild species, namely D. kutejensis (Hassk.) Becc. and Boschia excelsa Korth.. The DNA profile analysis was performed by using 10 RAPD primers. Furthermore, cluster analysis was done using the NTSYS (Numerical Taxonomic and Multivariate Analysis System) ver. 2.0. Observation of the DNA profile (DNA banding pattern) showed that all the primers succeeded in producing amplified DNA fragments. Of the total 78 bands produced, 10 bands were considered monomorphic, while 68 bands (87.20%) were considered polymorphic. The high level of polymorphism causes a low level of similarity between varieties so that not all resistant varieties are grouped in the same cluster. This study found that the 1kb band produced by the OPA-2 primer was a potential gen associated with resistance to P. palmivora. It is suggested to carry out further tests on crosses of resistant and susceptible varieties.

Potensi dan Keragaman Bakteri Endofit sebagai Agens Pemacu Pertumbuhan dan Biokontrol Anggrek

Soft rot disease in orchid plants is a factor in decreasing orchid production. One way of biological control that has the potential to spur growth is to utilize endophytic bacteria. This study aims to describe the diversity of orchid endophytic bacteria that have the potential as growth promoters and biocontrol agents. Observation parameters include indole acetic acid (IAA) production, inorganic phosphate dissolution, ammonia production of orchid endophytic bacteria, and antagonism of endophytic bacteria to pathogenic bacteria that cause soft rot in vitro. The diversity of orchid endophytic bacteria was analyzed using rep-PCR with BOX-A1R primer. The results showed that 10 isolates of orchid endophytic bacteria were able to produce IAA with a concentration of 79–321 μg/mL, able to dissolve phosphate, and produce ammonia. In antagonism testing against soft rot-causing bacteria, all isolates were able to form an inhibitory zone with a diameter of 3–7.2 cm. Furthermore, diversity analysis using rep-PCR showed that isolates of endophytic bacteria DnPh5, BgCt2, BgVt10, DnLp7, DnBl1, and DnAr4 had a uniform DNA band pattern so that they were grouped together. Meanwhile, isolates of TbPh7, IbtPhm1, DnDr2, and AkOc1 showed different DNA band patterns, indicating that the four isolates were different species or subspecies of bacteria. In dendrogram analysis, DnPh5, BgCt2, BgVt10, DnLp7, DnBl1, and DnAr4 isolates have a similarity of 100%. The similarity of isolates IbtPhm1, DnDr2, and AkOc1 was 90%, 79%, and 68%, respectively, against the other six isolates. TbPh7 isolate is an isolate with a low level of similarity to other isolates, which is about 51%.
 
 Keywords: orchid, endophytic bacteria, growth promoter, biocontrol agent, rep-PCR

IDENTIFICATION OF THE MOLUCCAN MEGAPODE (Eulipoa wallacei) NATURAL HABITAT IN HARUKU ISLAND, INDONESIA AND ITS VEGETATION COMPOSITION

The characteristics of island vegetation greatly influence the activities of endemic birds in island areas, such as the Moluccan endemic megapodes (Eulipoa wallacei) on Haruku Island. Therefore, it is essential to identify the specific location of the habitat utilized by individual birds for their daily activities on Haruku Island and to analyze the composition of the vegetation and the variety of plant species. Identification of bird habitat locations using radio-tracking on four newly hatched chicks and four adult birds. A total of 330 individual tracking points were recorded during the study period. The vegetation sample used a total of 420 plots for seedlings, saplings, poles, and trees which were then analyzed for importance value index (IVI), diversity, evenness, and similarity. We found that the Tanjung Maleo forest was their nesting habitat, while the Marunimei and Lalean forests were their daily habitats. A total of 91 plant species and 60 plant families were discovered with the vegetation diversity value of the three habitats was moderate (H’mean = 3.07) and tended to be dominated by air plant (Kalanchoe pinnata), sword fern (Nephrolepsis exalta), cogongrass (Imperata cylindrica), coco-grass (Cyperus rotundus), Indian camphorweed (Pluchea indica), and lanzone (Lansium domesticum) (Emean = 0.88), and have a relatively low level of species similarity between habitats (SImean = 38.30%). We found that the daily habitat of the Moluccan megapode on Haruku Island was around their nesting sites and has a complex structure because it was composed four vegetation strata. Therefore, for conservation purposes, habitat management must prioritize preserving forest habitats around the bird nesting sites.

An evaluation of Google Translate for Sanskrit to English translation via sentiment and semantic analysis

Google Translate has been prominent for language translation; however, limited work has been done in evaluating the quality of translation when compared to expert translators. Sanskrit, one of the oldest written languages in the world was added to the Google Translate engine in 2022. Sanskrit is known as the mother of North Indian languages such as Hindi, Punjabi, and Bengali. Sanskrit has been used for composing sacred Hindu texts such as the Bhagavad Gita and the Upanishads. In this study, we present a framework that evaluates Google Translate for Sanskrit using the Bhagavad Gita. We first published a translation of the Bhagavad Gita in Sanskrit using Google Translate and then compared it with selected prominent translations by experts. Our framework features a BERT-based language model that implements sentiment and semantic analysis. The results indicate that there is a low level of similarity between the Bhagavad Gita by Google Translate and expert translators in terms of sentiment and semantic analyses. We found major inconsistencies in the translation of philosophical terms and metaphors. We further implemented a qualitative evaluation and found that Google Translate was unsuitable for the translation of certain Sanskrit words and phrases due to the poetic nature, contextual significance, metaphor and imagery. The mistranslations are not surprising since the Bhagavad Gita is known as a difficult text not only to translate but also to interpret since it relies on contextual, philosophical and historical information. It is difficult to distinguish different names and philosophical concepts such as karma and dharma without knowing the context and having a background of Hindu philosophy. Our framework lays the foundation for the automatic evaluation of other languages that can be translated by Google Translate.

Genomes of Single-Stranded DNA Viruses in a Fecal Sample from South Polar Skua (Stercorarius maccormicki) on Ross Island, Antarctica.

South polar skuas migrate from subtropical regions to breed along coastal Antarctica. In a fecal sample collected on Ross Island, Antarctica, we identified 20 diverse microviruses (Microviridae) that share low levels of similarity to currently known microviruses; 6 appear to use a Mycoplasma/Spiroplasma codon translation table.

Comparison of ground insects diversity in cikaweni and canopy PPKA bodogol sukabumi tracks, west java

Nature Conservation Education Center (PPKA) Bodogol is one of the utilization zones that plays a role in preserving biodiversity. The purpose of this research was to explore the comparison of diversity and diversity index of ground insects in the Cikaweni and Canopy PPKA Bodogol, Sukabumi. The method used in this research is line transect by making a 500 m long transect line and divided into 10 plots. Each plot measures 2.5m x 2.5m, with a distance between plots of 50 m. Data processing was carried out using the Shannon-Wiener index, Eveness and similarity index. The results we got in this study found 33 individuals from 23 species of ground insects. In the Cikaweni track, the diversity value is 2.31 and the evenness index is 0.89, while in the canopy track the diversity value is 2.14 and the evenness index value is 0.93. These results indicate that both pathways belong to the moderate category without any dominating species. While the similarity index of the two tracks was 19% with only 3 species found in both tracks, namely Acheta sp., Blattella sp., and Euborellia annulipes, which means that both tracks have a low level of similarity.

General patterns of macrozoobenthos distribution in two rivers basins of the Khabarovsky Krai (Far East of Russia)

This article analyses the distribution patterns of macrozoobenthos in watercourses of the basins of the River Bajal and River Anyuy (Khabarovsky Krai, Russia) on the territories of the Bajal Sanctuary and Anyuy National Park. The distance-based linear models (DistLM) method was used to estimate the proportion of distribution of macroinvertebrates explained by the factors considered in the study (river basin, current velocity, substrate, channel width, temperature, pH). All of these factors contributed significantly, together explaining about one-third of the variability of macroinvertebrate distribution. The main explanatory factors were river basin and substrate (9.3% and 10.5%, respectively), as well as the current velocity (5.7%). Based on the cluster analysis, eight statistically significant groups of samples on the basis of similarity of taxonomic composition were identified. A set of indicator taxa was determined for each group and their indicator values were found. Using the Kruskal-Wallis analysis, the environmental factors significantly differing between the obtained groups and subgroups were singled out. There are well-defined patterns in the confinement of taxonomic complexes to certain habitats. Local environmental factors are the strong filter influencing the formation of taxonomic communities. The factor of belonging to the river basin also plays a significant role in the formation of invertebrate communities, which should be considered in the planning of monitoring studies on a large spatial scale. However, the distinguished groups and subgroups are characterised by a low level of internal similarity. Only about a quarter of the total species number belongs to indicator taxa, and samples do not form discrete clusters with obvious hiatus on the ordination diagram. The longitudinal distribution of macroinvertebrates for each river can be characterised as a punctuated gradient.

Isolation, Characterization, and Genome Analysis of a Novel Bacteriophage, Escherichia Phage vB_EcoM-4HA13, Representing a New Phage Genus in the Novel Phage Family Chaseviridae.

Shiga toxin-producing Escherichia coli (STEC) is one of the leading causes of foodborne illnesses in North America and can lead to severe symptoms, with increased fatality risk for young children. While E. coli O157:H7 remains the dominant STEC serotype associated with foodborne outbreaks, there has been an increasing number of non-O157 STEC outbreaks in recent years. For the food industry, lytic bacteriophages offer an organic, self-limiting alternative to pathogen reduction-one that could replace or reduce the use of chemical and physical food processing methods. From EHEC-enriched sewage, we isolated a novel bacteriophage, vB_EcoM-4HA13 (4HA13). Phenotypic characterizations revealed 4HA13 to possess a myoviral morphotype, with a high specificity to non-motile O111 serotype, and a long latent period (90 min). Through genomic analyses, this 52,401-bp dsDNA phage was found to contain 81 CDS, but no detectable presence of antibiotic resistance, integrase, or virulence genes. A BLASTn search for each of the identified 81 CDS yielded homologues with low levels of similarity. Comparison of RNA polymerase and terminase large subunit amino acid sequences led to the proposal and acceptance of a new bacteriophage family, Chaseviridae, with 4HA13 representing a new species and genus. The discovery of this phage has broadened our current knowledge of bacteriophage diversity.

In silico studies disclose the underlying link between binding affinity and redox potential in laccase isoforms

Laccases are copper-containing enzymes belonging to the family of multicopper oxidases (MCOs). All MCOs use molecular oxygen to oxidize a wide range of organic compounds by radical catalysis. One of the key fundamental properties of laccases is having high or low redox potentials depending on the active site organization. Several experimental studies have been done to rationalize the high and low redox potential laccases (LRPL), however, molecular understanding is still lacking. In this work, we explored the proteomic profile of laccases produced in the fungal cultures, specifically induced with lignocellulosic biomass such as rice straw. This study was undertaken to explain the differences in the high redox and low redox potential values of different laccases using in-silico approaches. Proteomic profiling and structural and sequence analysis revealed a low level of similarity among them. Docking analyses and molecular dynamics simulation analysis revealed that high redox potential laccases (HRPL) are having good binding affinity compared to low or medium redox potential laccases (MRPL). The stability of these complexes was further analyzed based on reactive distances, active site volume comparison and a number of tunnel formations that were observed to be significantly higher for HRPL. Our results indicate that the number of tunnel formations calculated from the simulation’s trajectories and available water molecules at the T3 site directly correlates with the laccases’ redox potentials. This study will be helpful and provide valuable inputs for the designing of new laccases to improve lignin degradation. Communicated by Ramaswamy H. Sarma

Cutaneous papilloma associated with a novel papillomavirus sequence in a cat.

A 5-mm diameter mass developed on the nasal planum of a 4.5-y-old castrated male domestic shorthaired cat; the mass was raised ~2 mm above the surrounding skin. Histology revealed focal thickening of the epidermis with marked orthokeratosis. Many of the epidermal cells within the mass had prominent papillomavirus-induced changes. A diagnosis of a viral papilloma was made, and a DNA sequence from a novel papillomavirus type was amplified from the lesion. Although the sequence was most similar to other feline papillomavirus types, the low level of similarity was suggestive of a novel papillomavirus genus. There has been no recurrence of the mass or development of additional lesions in the 6 mo since the mass was removed. This is the third cutaneous papilloma reported in a cat; a putative feline papillomavirus type has not been identified previously within these lesions, to our knowledge. Our findings expand the range of lesions associated with papillomaviruses in cats and increase the number of papillomavirus types that infect cats.