Distinct Species Research Articles

Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.

Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging. We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences. The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation. We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.

Oxynoemacheilus kottelati, a new species from the Havran and Karınca streams in Northern Aegean Basin, Türkiye (Teleostei, Nemacheilidae)

The taxonomic status of the Oxynoemacheilus from the Karınca and Havran streams in the north Aegean Basin was evaluated, and it was concluded that these populations contain a new species. The new species, Oxynoemacheilus kottelatisp. nov., is distinguished by a body with a marbled pattern, a deeper caudal peduncle, a shorter caudal peduncle, a wider interorbital distance, and a shorter middle caudal-fin lope. Oxynoemacheilus kottelatisp. nov. is differentiated from the closest species, O. marmaraensis, in possessing 51 nucleotide substitution sites, a genetic distance of 8.40%, the presence of an axillary lobe at the base of the pelvic fin (vs. absent), and a narrower median incision in the upper lip (vs. absent). Three species delimitation tests (ASAP, ABGD, and PTP) and phylogenetic analyses reinforce the validity of O. kottelatisp. nov. as a distinct species.

Morphological and Molecular Characters Differentiate Common Morphotypes of Atlantic Holopelagic Sargassum

Since 2011, massive new strandings of holopelagic Sargassum have been reported on the coasts of the Caribbean, northern Brazil, Guiana, and West Africa, causing severe economic and ecological damage. Three common morphotypes (S. fluitans III, S. natans I, and S. natans VIII) were identified as responsible for these catastrophic events, with dominance shifts between them over time. However, the taxonomic status of these holopelagic Sargassum morphotypes remains unclear. Using an integrative taxonomy framework, combining a morphological study and molecular analyses, this study aimed to clarify their taxonomic status. Morphological analyses of 54 characters revealed no intermediate form between the three morphotypes, with the overall shape, nature of the axis, and size and shape of blades and vesicles being the most discriminating. An analysis of mitochondrial (IGS, cox2, cox3, mt16S rRNA, and nad6) and plastid (rbcL) markers confirmed the genetic divergence among the three morphotypes, with a lower level of divergence between the two S. natans morphotypes. Without additional molecular characterization, these morphotypes cannot be classified as three distinct species. However, due to their distinct morphological characteristics and sympatry within drifting aggregations, a revision of holopelagic species names is proposed, with Sargassum fluitans var. fluitans (for S. fluitans III), Sargassum natans var. natans (for S. natans I), and S. natans var. wingei (for S. natans VIII). This revision provides necessary clarity on the species involved in inundations of the tropical Atlantic.

New Understanding of Meta-Topolin Riboside Metabolism in Micropropagated Woody Plants.

Topolin cytokinins have emerged as valuable tools in micropropagation. This study investigates the metabolism of meta-topolin riboside (mTR) in three distinct tree species: Handroanthus guayacan and Tabebuia rosea (Bignoniaceae), and Tectona grandis (Lamiaceae). Employing labeled N15 mTR, we unraveled the complex mechanisms underlying cytokinin homeostasis, identifying N9-glucosylation as the principal deactivation pathway. Our findings demonstrate a capacity in T. rosea and H. guayacan to reposition the hydroxyl group on the cytokinin molecule, a previously unexplored metabolic pathway. Notably, this study reveals remarkable interfamilial and interspecies differences in mTR metabolism, challenging established perspectives on the role of callus tissue in cytokinin storage. These insights not only illuminate the metabolic intricacies of mTR, a cytokinin with interesting applications in plant tissue culture, but also enhances our understanding of cytokinin dynamics in plant systems, thereby enriching the scientific discourse on plant physiology and cytokinin biology.

Enhancing salt marshes monitoring: Estimating biomass with drone-derived habitat-specific models

Salt marshes play a vital role in biodiversity conservation, coastal protection, and carbon sequestration. Estimating aboveground biomass (AGB) is crucial for quantifying the carbon sequestration capacity of the system. However, traditional fieldwork methods are time-consuming, demanding, and detrimental to marsh ecosystems. In this study, we propose utilizing low-altitude remote sensing techniques to collect high-resolution LiDAR and multispectral (MS) data for biomass assessment. With these datasets, we characterized salt marsh vegetation habitats through the analysis of vegetation indices (VIs) variability. LiDAR high-resolution topographic information aids in evaluating habitat distribution. Moreover, the Anthocyanin Reflectance Index 2 (ARI2), combined with the Digital Surface Model, allows for the identification and separation of the two habitats with distinct dominant species (Sarcocornia spp. and Sporobolus maritimus). The analysis of the annual cycle of VIs reveals the presence of seasonality. However, the VIs for the two vegetation classes exhibit dissimilar seasonal changes, indicating distinct growth mechanisms for each. Biomass models are created for each season in the annual cycle. Habitat-specific models exhibit higher precision (up to 99%) than models that treat species uniformly. Depending on whether the marsh is considered as a whole or separated into dominant habitats, differences in biomass estimation trends are observed. This implies that the two dominant species exhibit varying behaviours throughout the year, contributing to diverse biomass production. The study reveals a seasonal pattern in the total AGB, with the highest biomass value in summer and the lowest peak in spring, with annual variation accounting for only 9% of total output. The reduced AGB value in spring may be due to increased soil salinity and stress. The use of LiDAR and MS data from an unmanned aerial vehicle (UAV) is crucial for accurately distinguishing primary marsh habitats and creating detailed biomass models, with unprecedented accuracy. This method is user-friendly, repeatable, and cost-effective, enabling the study of salt marshes, evolutionary trends, and climate change response requiring less fieldwork.

Real Time Recognition of Underwater Images using Deep Learning

This study focuses on the development of an effective image recognition system tailored for underwater environments. The objective is to create a robust and efficient artificial neural network capable of accurately categorizing underwater images amidst challenges like noise, distortion, and variable lighting conditions. The system's primary function is to classify images into predefined categories, such as distinct species of marine organisms, underwater objects, or environmental conditions.

Occurrence of Dictyosphaeria (Cladophorales, Chlorophyta) species on the Brazilian coast and oceanic islands, based on morphological and molecular data

Abstract Molecular data related to morphology from the multicellular vesiculated genus Dictyosphaeria are scarce. We provide the first molecular data on Dictyosphaeria species from the southwestern Atlantic Ocean, sampled from the Brazilian northeastern coast, and two oceanic islands (Trindade, southeastern Brazil, and Fernando de Noronha, northeastern Brazil). The samples from Brazil were morphologically identified as Dictyosphaeria versluysii and D. ocellata. Our newly generated sequences of D. versluysii formed a monophyletic clade, while their relationship with D. versluysii from the Indo-Pacific Ocean, where the type locality of the species is located, was unresolved. Additionally, the newly generated sequences of D. ocellata confirm its status as a distinct species but reinforce the difficulties in morphologically separating this species. These results might be indicative of cryptic diversity in D. versluysii and highlight the need for molecular data from other geographic locations to understand the diversity and distribution of Dictyosphaeria species.

Plasma miR-19b, miR-34a, and miR-146a expression in patients with type 2 diabetes mellitus and cataract: A pilot study.

Cataract is among the most common ocular complications in diabetes mellitus (DM). While microRNA (miRNA) dysregulations in DM have been previously reported, consensus is still lacking concerning miRNA expression in cataract. Furthermore, the miRNA profile in diabetic cataract patients remains largely unexplored, and data on plasma expression levels are limited. Our study aimed to assess the plasma levels of three distinct miRNA species (hsa-miR-19b, hsa-miR-34a, and hsa-miR-146a) implicated in the development of cataract and/or DM.We investigated the circulating miRNA expression in DM patients diagnosed with cataract, compared to a non-DM cataract group. We employed qRT-PCR for relative quantification experiments and subsequently conducted a correlation analysis between miRNA expression levels and clinical characteristics. Our findings reveal that hsa-miR-34a and hsa-miR-146a are differentially expressed in the two cohorts. However, no significant correlation was observed between the clinical variables and miRNA levels. In summary, our results suggest a potential role for hsa-miR-34a and hsa-miR-146a in the biology of diabetic cataract.

Ecological observations of freshwater snails in the vicinity of an artificial lake

This investigation delves into the ecological dimensions of freshwater snails in the vicinity of an artificially created lake. The aim of this research was to comprehend the distribution, prevalence, and variety of freshwater snail species within the ecosystem surrounding the manmade lake. The study spanned from August to November 2023, conducted at three distinct sample stations (I, II, and III), with bi-weekly sample collections. Standard keys were employed for the identification of snails, and the Shanon-Weiner and Simpson's similarity indices were used to explore the diversity of snail species. Throughout the study, a total of 311 individuals representing three distinct species encountered in this study were documented. Acathina fulica exhibited the highest abundance (129 individuals), while Pomacea bridgesii displayed the lowest abundance (66 individuals). The month of August registered the highest population (122 individuals), contrasting with the lowest count in November (37 individuals). Abundance varied across stations, with Station II recording the lowest (77 individuals) and Station III the highest (116 individuals). Regarding diversity, Pomacea bridgesii emerged as the most diverse species (0.3670 & 0.3662), while Littorina littorea exhibited the least diversity (0.0000) across the stations. This investigation contributes valuable insights into the dynamics of freshwater snail populations in the periphery of artificial lakes, shedding light on their distribution patterns and ecological interactions.

Clypeina? pamelareidae n. sp., a new dasycladalean alga from the Upper Triassic of Lime Peak (Yukon, Canada)

A new calcareous alga is described from the Norian limestones of Lime Peak, Yukon, Canada. The algae-bearing limestones were formed in a low-energy environment below the storm wave base, as indicated by the abundance of carbonate mud. Clypeina? pamelareidae n. sp. usually appears in the form of separate laterals scattered in the sediment. The laterals are pyriform, with the tip slightly curved upwards. Sometimes they are arranged around a non-calcified axial cavity. The lack of calcification of the connection between the main axis and the laterals led to the detachment and scattering of the latter in the sediment. The shape of the laterals and their arrangement are reminiscent of the genus Clypeina (Michelin). Still, the lack of completely preserved specimens leads us to attribute it with uncertainty to this genus. Almost certainly, the alga in question is individualised as a new distinct species, basically different from other Mesozoic or Cenozoic species of the genus, as well as from the only species of Clypeina known from the Triassic (Clypeina besici Pantic).

Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region

Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.

Analysis of spore prevalence and sporulation potential in prepackaged meat products

Spores are recognized as significant factors affecting the safety of prepackaged meat products. However, current knowledge about the prevalence and distribution of spores in these products is limited. This study investigated 360 commonly consumed prepackaged meat products sourced from Zhengzhou, Henan Province, to assess spore prevalence, species, and characteristics. Using the 16S rRNA method, primary spore species were isolated and identified. The results revealed a spore prevalence of 60.6% (218/360), identifying eight distinct bacterial species. In laboratory cultivation, Bacillus. subtilis exhibited the highest spore sporulation efficiency at 95.1%, indicating a significant foodborne risk. Under the storage condition of -4 °C, the spore in food (starch sausage) maintained stable dormant state within 60 days. Additionally, Raman spectroscopy was employed to analyze the biochemical components of the cultured spores, accurately classifing eight species of spores using linear discriminant analysis (LDA). The high percentage of spore contamination in prepackaged meat products poses a potential health risk to consumers. An enhanced understanding of spore prevalence, sporulation potential, and storage methods in these products can empower industries to adjust measures effectively, controlling spore pollution in meat products.

MARC1 in MASLD: Modulation of lipid accumulation in human hepatocytes and adipocytes.

Mutations in the gene MTARC1 (mitochondrial amidoxime-reducing component 1) protect carriers from metabolic dysfunction-associated steatohepatitis (MASH) and cirrhosis. MTARC1 encodes the mARC1 enzyme, which is localized to the mitochondria and has no known MASH-relevant molecular function. Our studies aimed to expand on the published human genetic mARC1 data and to observe the molecular effects of mARC1 modulation in preclinical MASH models. We identified a novel human structural variant deletion in MTARC1, which is associated with various biomarkers of liver health, including alanine aminotransferase levels. Phenome-wide Mendelian Randomization analyses additionally identified novel putatively causal associations between MTARC1 expression, and esophageal varices and cardiorespiratory traits. We observed that protective MTARC1 variants decreased protein accumulation in in vitro overexpression systems and used genetic tools to study mARC1 depletion in relevant human and mouse systems. Hepatocyte mARC1 knockdown in murine MASH models reduced body weight, liver steatosis, oxidative stress, cell death, and fibrogenesis markers. mARC1 siRNA treatment and overexpression modulated lipid accumulation and cell death consistently in primary human hepatocytes, hepatocyte cell lines, and primary human adipocytes. mARC1 depletion affected the accumulation of distinct lipid species and the expression of inflammatory and mitochondrial pathway genes/proteins in both in vitro and in vivo models. Depleting hepatocyte mARC1 improved metabolic dysfunction-associated steatotic liver disease-related outcomes. Given the functional role of mARC1 in human adipocyte lipid accumulation, systemic targeting of mARC1 should be considered when designing mARC1 therapies. Our data point to plasma lipid biomarkers predictive of mARC1 abundance, such as Ceramide 22:1. We propose future areas of study to describe the precise molecular function of mARC1, including lipid trafficking and subcellular location within or around the mitochondria and endoplasmic reticulum.

Chitinozoan response to the ‘Kellwasser events’: population dynamics and morphological deformities across the Frasnian–Famennian mass extinction

AbstractFossil (zoo)plankton dynamics during Devonian ocean‐anoxic and extinction events can shed light on the palaeoceanographic and geochemical processes that shaped the middle Palaeozoic biosphere. However, datasets on (Upper) Devonian marine palynology, illustrating such dynamics, remain underexplored. The type section of the Sweetland Creek Shale in Iowa (USA) offers a detailed conodont zonation for the upper Frasnian and across the Frasnian–Famennian boundary, records the Upper and Lower Kellwasser events and has pristine preservation of organic material, making this an ideal section to study the effects of this catastrophic event on chitinozoan zooplankton populations. A total of 3998 specimens were recovered, imaged and classified into 12 distinct species, 10 of which were previously unknown. This study demonstrates the unrealized potential of chitinozoans as a regional biostratigraphic tool in the Upper Devonian. The Lower Kellwasser Event is characterized by a drop in chitinozoan abundance and the run up to the Upper Kellwasser Event marks a period of rapid species turnover rates. Interestingly, every assemblage in this interval is nearly monospecific. Patterns of changing spine morphologies in Fungochitina pilosa, Ramochitina sp. A and Saharochitina sp. A are herein explored as potential ecophenotypic expressions. We identify Angochitina monstrosa as a new disaster species. The discovery of two teratological chitinozoans specimens, in combination with the presence of the disaster species Angochitina monstrosa and deformation in contemporaneous conodonts, supports our previous discovery that marine teratology is a feature of many Palaeozoic extinction events, possibly triggered by the injection of hydrothermal brines into the ocean.

The long‐beaked common dolphin of the eastern Pacific Ocean: Taxonomic status and redescription of Delphinus bairdii

AbstractNeritic, long‐beaked common dolphins have been described as species distinct from the more oceanic and globally distributed short‐beaked species, Delphinus delphis, although recent molecular studies have challenged this view. In the eastern North Pacific (ENP), the taxonomic status of the long‐beaked (bairdii) form has been controversial since its original description in 1873, and has vacillated between species, subspecies, and geographic forms several times. It is currently provisionally viewed as a subspecies of Delphinus delphis, D. d. bairdii. To clarify this situation, we reviewed the literature and conducted additional analyses using both newly obtained genetic and cranial morphometric data sets. The results indicate that there are diagnostic differences in skull morphology and coloration between the eastern Pacific long‐and short‐beaked forms, and near‐perfect diagnosability in mitochondrial DNA. These differences, along with indications of ecological distinctions, including important differences in life history parameters and reproductive timing, indicate that these forms are well on their way down separate evolutionary pathways. As such, we consider them to be distinct species in the eastern Pacific. The long‐beaked species is referable to Delphinus bairdii Dall, 1873, and is redescribed as such herein.

Taxonomy of Naumann’s and dusky, red-throated and black-throated thrush complexes (Aves: Turdidae) using morphological and molecular characteristics

Abstract Species are the basic units in evolution and biodiversity and thus a reasonable species classification is essential to assess and protect biodiversity. The classifications of the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes are not well defined in Turdidae (Aves, Passeriformes). Herein, we use qualitative and quantitative morphological characters and molecular data to review the taxonomy of these thrush complexes. These four thrushes can be distinguished with qualitative features of feather color and striping. These birds cannot be divided by quantitative features, which only work on two groups of thrush complexes. Phylogenetic analysis based on mitochondrial genes indicate that all haplotypes might be divided into two monophyletic clades corresponding to two groups of thrush complexes. According to coalescence-based species delimitation and the gen-morph species concept, these two groups of thrush complexes should be separated as two distinctive species (T. naumanni and T. ruficollis) and including two subspecies per species. This species classification is also supported by gene flow analysis. There is a significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis using a few microsatellite loci. This leads to a pattern of nuclear-mitochondrial discordance between the two birds that can be explained by several potential mechanisms. This study provides the first comprehensive classification of the two thrush complexes on a population level using morphological and molecular characteristics, which will be useful in expanding our understanding of species division among thrush complexes.

Aspleniumguodanum (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny.

A new spleenwort species, Aspleniumguodanum, was found and described from Danxia landform region in Guangdong, China. The new species has close resemblance to A.subcrenatum Ching ex S.H.Wu in morphology, but can be distinguished by having plants small, stipes and rachises not covered with fibrous scales, relatively fewer pairs of pinnae, pinnae short, pinna margin weakly biserrate, pinna apex acute and lower pinnae obviously reduced. Phylogenetic analyses, based on six plastid markers (atpB, rbcL, rps4 & rps4-trnS and trnL & trnL-F) of the new species and its relatives, support a close relationship between A.guodanum and A.subcrenatum. Only one population with no more than 50 individuals were found and, therefore, it is recommended to be classified as Critically Endangered (CR) following IUCN Red List Criteria.

Staphylococcus aureus Isolated From Traditional Artisanal Raw Milk Cheese from Southern Brazil: Diversity, Virulence, and Antimicrobial Resistance Profile

Staphylococcus aureus is one of the primary pathogenic agents found in cheeses produced with raw milk. Some strains of S. aureus are enterotoxigenic, possessing the ability to produce toxins responsible for staphylococcal food poisoning when present in contaminated foods. This study aimed to genotypically characterize, assess the antimicrobial resistance profile, and examine the enterotoxigenic potential of strains of S. aureus isolated from artisanal colonial cheese. Additionally, a bacterial diversity assessment in the cheeses was conducted by sequencing the 16S rRNA gene. The metataxomic profile revealed the presence of 68 distinct species in the cheese samples. Fifty-seven isolates of S. aureus were identified, with highlighted resistance to penicillin in 33% of the isolates, followed by clindamycin (28%), erythromycin (26%), and tetracycline (23%). The evaluated strains also exhibited inducible resistance to clindamycin, with nine isolates considered multidrug-resistant (MDR). The agr type I was the most prevalent (62%) among the isolates, followed by agr type II (24%). Additionally, ten spa types were identified. Although no enterotoxins and their associated genes were detected in the samples and isolates, respectively, the Panton-Valentine leukocidin gene (lukS-lukF) was found in 39% of the isolates. The presence of MDR pathogens in the artisanal raw milk cheese production chain underscores the need for quality management to prevent the contamination and dissemination of S. aureus strains.

GCMS-based Phytochemical Profiling of L. camara Induces Apoptosis and Cell Cycle Arrest in Lung Cancer

In this paper, the focus is on the phytochemical study of Lantana camara L. leaf extract, specifically its antioxidant and anti-cancer effects. The study shows that all solvent extracts have significant antioxidant and anticancer activity. However, the methanol liquid extract of L. camara leaf contains higher levels of metabolites than other solvents. The methanolic extracts of the leaves of four distinct species of Lantana camara also have high levels of terpenoid chemicals, which demonstrate strong antioxidant and free radical elimination properties. With further research, it is possible that useful medications can be developed for the treatment of various human diseases, especially lung cancer.

Taxonomic resurrection of Saxifraga lancangensis (Saxifragaceae)

BackgroundAccurate species delimitation is fundamental for testing evolutionary theory and provides essential implications for conservation management. The arctic-alpine genus Saxifraga L. (Saxifragaceae) is taxonomically complex and many species have not been critically assessed. The taxonomic and phylogenetic status of Saxifraga lancangensis Y.Y.Qian, considered as a synonym of Saxifraga mengtzeana Engl. & Irmsch. in previous studies, is re-evaluated in light of new evidence presented here.ResultsEvidence from morphological comparison and sequencing of plastid genome indicate that S. lancangensis belongs to Saxifraga sect. Irregulares Haw., and is closely related to Saxifraga geifolia Balf.f., and S. mengtzeana. However, S. lancangensis can be diagnosed by its petals with red and clawless base, leaf blade orbicular and leaf margin shallowly dentate.ConclusionsThe morphological and molecular evidence support the resurrection of S. lancangensis as a distinct species. An updated morphological description based on protologue and fresh material, diagnostic characters, and original photographs of the resurrected species are presented.