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The taxonomic status of butterfly rays within the genus Gymnura remains a subject of ongoing debate among researchers. Some authors recognize up to five valid species for the Americas, while others considered several to be synonyms, which has posed a persistent challenge. We aimed to shed light on this complexity by employing molecular operational taxonomic units (MOTUs) based on the mitochondrial gene cytochrome oxidase I (COI). Genetic sequences were obtained from fresh muscle tissue collected in the marine ecoregions corresponding to the type locality from all the nominal butterfly ray species distributed along the Eastern Tropical Pacific (ETP). Our results unveiled compelling findings; all the species delimitation models used consistently identified seven MOTUs for the American continent and an extra G. altavela MOTU restricted to Africa. In addition, our results and models exceeded the worldwide accepted interspecific threshold of 2.0%. Remarkably, our results support the taxonomic reinstatement of Gymnura afuerae (Hildebrand, 1946) as a valid species, with a range expanding into the ETP in the Southern Hemisphere. Similarly, our data support the recent suggestion of resurrecting Gymnura valenciennii (Duméril, 1865) as a valid species in the western Atlantic. These findings urge a reassessment of the conservation status and a comprehensive taxonomic revision of American butterfly rays. [ABSTRACT FROM AUTHOR]

Freshwater habitats in Indo-Pacific tropical islands are mainly inhabited by amphidromous fish, which display a marine larval phase while the rest of their life cycle takes place in rivers. Gobiiformes are the most diversified fish component in these ecosystems. In this study, we focused on the status of the widespread Stenogobius genus (Gobioidei). This genus is distributed from the Indian Ocean to French Polynesia. Recently, a first revision of Stenogobius was undertaken leading to the redescription of S. genivittatus (Valenciennes, 1837) and the placement of 12 species names as synonyms of this species. This paper focuses on the status of nine Stenogobius species supposedly present in Indonesia, a country well known as one of the freshwater hotspots of biodiversity. The present study is based on 95 specimens, and includes morphomeristic data and partial mitochondrial COI sequences. Our results show that, at least four species occur in Indonesia, including the widespread species S. genivittatus. [ABSTRACT FROM AUTHOR]

The genus Pangora Moore (1879) is endemic to south Asia, with four known species distributed in India, Sri Lanka, and Nepal. The current study offers the scientific community the first mitochondrial genome sequence of the known species Pangora matherana (Moore). The phenotypic and phylogenetic tree analysis reveals a new species, Pangora keralaensis Abhilash & Adarsh sp. nov., from India. The male genitalia and morphological analysis of the new taxa are also provided. A preliminary phylogenetic tree based on the mt COI DNA sequence is also provided for the new species and the known species, Pangora matherana (Moore, 1879).

We introduce topological conditions on a broad class of functionals that ensure that the persistent homology modules of their associated sublevel set filtration admit persistence diagrams, which, in particular, implies that they satisfy generalized Morse inequalities. We illustrate the applicability of these results by recasting the original proof of the Unstable Minimal Surface Theorem given by Morse and Tompkins in a modern and rigorous framework. [ABSTRACT FROM AUTHOR]

The taxonomic status of butterfly rays within the genus Gymnura remains a subject of ongoing debate among researchers. Some authors recognize up to five valid species for the Americas, while others considered several to be synonyms, which has posed a persistent challenge. We aimed to shed light on this complexity by employing molecular operational taxonomic units (MOTUs) based on the mitochondrial gene cytochrome oxidase I (COI). Genetic sequences were obtained from fresh muscle tissue collected in the marine ecoregions corresponding to the type locality from all the nominal butterfly ray species distributed along the Eastern Tropical Pacific (ETP). Our results unveiled compelling findings; all the species delimitation models used consistently identified seven MOTUs for the American continent and an extra G. altavela MOTU restricted to Africa. In addition, our results and models exceeded the worldwide accepted interspecific threshold of 2.0%. Remarkably, our results support the taxonomic reinstatement of Gymnura afuerae (Hildebrand, 1946) as a valid species, with a range expanding into the ETP in the Southern Hemisphere. Similarly, our data support the recent suggestion of resurrecting Gymnura valenciennii (Duméril, 1865) as a valid species in the western Atlantic. These findings urge a reassessment of the conservation status and a comprehensive taxonomic revision of American butterfly rays.

Classification of design codes by the level of complexity of their design was cre-ated for the first time. The obtained results are key to understanding the role of the QR code as a full-fledged work of art in the context of modern design. In the future, this will allow us to single out the most noticeable trends in the development of coded information in the conditions of modern visual culture.

Alternaria black spot of pomegranate (Punica granatum) was reported for the first time in Italy. In spring 2023, an outbreak of this disease was noticed in commercial pomegranate 'Wonderful' orchards of the municipality of Misterbianco (Sicily), following an unusually rainy period. A total of 30 randomly selected Alternaria isolates recovered from typical necrotic spots of leaves and fruits were characterized. Based on the colony morphology on solid agar media (PDA and MEA), isolates were separated into three distinct morphotypes (1, 2, and 3). The first two morphotypes comprised only isolates from fruits, while morphotype 3 comprised only isolates from leaves. Multigene phylogenetic analysis of four DNA regions, including internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a SCAR marker (OPA10–2), identified the isolates of morphotypes 1 and 2 as Alternaria alternata and morphotype 3 isolates as A. arborescens. In pathogenicity tests on unwounded leaves and fruit, the isolates of all three morphotypes produced symptoms on the leaves of three pomegranate cultivars, 'Acco', 'Wonderful', and 'Etna'. The symptoms on 'Acco' leaves were the least severe. Conversely, the fruits of 'Acco' were the most susceptible. The isolates of morphotypes 2 and 3 were not pathogenic on the fruits of 'Wonderful' and 'Etna'. This is the first report of Alternaria black spot in Italy and of A. arborescens associated with Alternaria black spot of pomegranate worldwide. [ABSTRACT FROM AUTHOR]

In a recent study based on the generalized mixed Yule coalescent method for delimiting species, a threshold of 2% genetic distance using cytochrome c oxidase subunit I sequences was used to delimit the species of Microglanis. That action resulted in assembling several populations of Microglanis from Atlantic coastal rivers between Rio Grande do Sul and São Paulo states as a single species, Microglanis cottoides, including Microglanis cibelae as a junior synonym. We reexamined these populations and found three species diagnosed by their morphology and that constitute separate mtDNA lineages, including a new species. The synonym of M. cibelae and M. cottoides is reviewed and refuted based on morphological and molecular evidence. M. cibelae and the new species are sympatric and occasionally syntopic in the Tramandaí, Mampituba, and Araranguá river basins. The new species is distinguished from M. cibelae and M. cottoides by the anterior margin of the posttemporosupracleitrum narrow articulated with the epioccipital, the short mental and maxillary barbels, and depressed head and body. [ABSTRACT FROM AUTHOR]

Acorrect classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short riboso)mal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80–92 % POCP values and a range of 60–70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. [ABSTRACT FROM AUTHOR]

Classification of design codes by the level of complexity of their design was created for the first time. The obtained results are key to understanding the role of the QR code as a full-fledged work of art in the context of modern design. In the future, this will allow us to single out the most noticeable trends in the development of coded information in the conditions of modern visual culture. [ABSTRACT FROM AUTHOR]

Using QR codes in school libraries can indeed be a valuable and innovative approach to enhance the utilisation of library resources and services. Implementing these strategies can create an interactive and engaging library experience, motivating students to visit the library more frequently and make the most of available resources. The study explains the various uses of QR codes in promoting school library resources and its services, with all possible implementations to maximize their use. It encourages freely available tools to generate QR codes. It also tries to show, how the school library at B.V.B. Vidyashram Pratapnagar uses QR codes to create an experience that makes students want to go there more often. [ABSTRACT FROM AUTHOR]

Ensuring the correct identification of the patient is key to matching the correct patients with the proper care (e.g. correct administration of medications and treatments), but it is also applied, for example, to monitoring the patient's movement in the hospital environment. This scoping review aims to find out what technologies based on unique patient identifiers are used to identify patients in healthcare facilities to increase patient safety and to identify future research trends. PRISMAScR guidelines were used, and the search focused on Web of Science and Scopus citation databases from 2000 to February 2024. Thirty-two papers dealing with patient identification methods from the point of view of person identification were found. The solutions found were built on the technologies (linear or 2D) of barcodes, RFID and NFC tags. None of the patient identification solutions found offer complete accuracy due to the human factor, and each solution targets a different problem context associated with a particular type of health facility. Future research can focus on the combination of multiple technologies, including biometric methods, to improve identification and tools to support decisions about the use of technology in a particular context and health facility (e.g. hospitals, medical nursing homes). [ABSTRACT FROM AUTHOR]

The increasing population growth in Indonesia also affects the need for a comfortable and safe shopping place. The increasing number of consumers at the same time causes lines, especially in the payment section. The purpose of this research is to try to develop a cashier with a self-service method to help speed up the payment process and reduce lines. This research uses a GM66 scanner to scan barcodes on product items to be purchased. While the 3200-DB TCS Sensor is used to detect the nominal money paid. Information on the price of goods that have been scanned is displayed on the LCD screen. After payment is complete, the shopping receipt will be printed. In the results of this study, a tool was obtained that can be used to automatically sum up the price of groceries. Additionally, this tool can also facilitate transactions for payment of groceries. However, in this study, the new payment transaction process can only use $50 bills, and there is no system for returning change.

Silverfish (Zygentoma) are an ancient, but poorly studied group of primitively wingless insects. Species definition based on morphology alone is complicated by variations arising from the continuous moulting, even after reaching sexual maturity. In recent studies the use of molecular data has supported the identification of consistent morphological character traits, however only a small fraction of the species have been investigated. Eight species of the large silverfish genus Acrotelsella, collected by the first author from the Cape York Peninsula of northeastern Australia, are described and named as new species. Molecular data (COI and 28S) are presented that reinforces previous suggestions that the genus will eventually need to be split into two.

This paper discusses the development of desktop applications for traceability systems. The application was developed to facilitate data recording and tracking in an electronics manufacturing company's storage process of Printed Circuit Board (PCB) products. The application is developed using the Visual Basic language and Microsoft Excel databases. Additionally, the application is integrated with a barcode scanner to simplify the data entry process from PCBs and employee ID cards. Through the trial process conducted on the developed application, it has generally functioned in accordance with the development goals. Program control validation has been tested through several application access attempts from users registered as operators and administrators. The application has successfully recorded data from inbound and outbound processes, demonstrating storage and tracking functionality. Furthermore, the application has displayed the actual status data of the PCBs present in the warehouse. In terms of user satisfaction, seven users stated that this application was effective and efficient compared to the manual data recording process previously used by the company. This result was obtained from a questionnaire after the application was implemented in the company warehouse.

The application of environmental DNA (eDNA) methods to simultaneously study vertebrate diversity holds promise to accelerate conservation efforts, especially in freshwater systems which are among the most imperiled in the world. Here, using eDNA sampling, we identify patterns of vertebrate biodiversity across different habitats of the Kankakee River watershed, one of the most diverse lotic systems in Illinois, USA. Our eDNA metabarcoding analyses identified 147 different taxa, including 77 fishes, 38 birds, 24 mammals, five amphibians and three reptiles at 11 locations in the watershed, including tributaries and mainstem stretches upstream and within the Kankakee River State Park protected area. When compared to seining, eDNA sampling consistently detected more fish species, including non-native and imperiled species. We also found that vertebrate communities among the different habitats significantly varied in taxonomic composition, showing an upstream-downstream shift along the mainstem river as well as tributary-specific assemblages. Our study demonstrates the ability of single-marker eDNA metabarcoding to simultaneously document aquatic and terrestrial communities across large temperate lotic ecosystems and to monitor diversity patterns across protected areas.

This paper describes four new species earthworms from Hunan and Anhui provinces, China, Amynthas xiangtanensis Qiu & Jin, sp. nov., Amynthas taoyuanensis Qiu & Jin, sp. nov., Amynthas xuanchengensis Jin & Li, sp. nov. and Metaphire donganensis Jin & Jiang, sp. nov. Amynthas xiangtanensis sp. nov., and A. taoyuanensis sp. nov. belong to the Amynthas corticis group. Both have four pairs of intersegmental spermathecal pores in 5/6–8/9; male pores in segment XVIII, separated by 1/3 of body circumference, each on top of a slightly raised porophore, surrounded by several tiny genital papillae. Amynthas taoyuanensis sp. nov. prostate glands are degenerated. Amynthas xuanchengensis sp. nov. belongs to the Amynthas morrisi group, it has two pairs of spermathecal pores in 5/6 and 6/7; male pores in XVIII, separated by 1/3 of body circumference, each on top of a slightly raised, circular porophore. Metaphire donganensis sp. nov. belongs to the Metaphire houlleti group. It has three pairs of spermathecal pores in 6/7–8/9; male pores in XVIII, separated by 1/3 of body circumference, each on the bottom center of the longitudinal copulatory chamber. [ABSTRACT FROM AUTHOR]

Simple Summary: Hoverflies, also known as flower flies, are a highly diverse group of two-winged flies with more than 6000 known species worldwide. This group of insects plays an important role in ecosystems, providing services such as plant pollination and pest control, among others. Regarding Eumerus, this hoverfly genus is one of the most speciose in the Palaearctic region, where new species are continually being discovered. Nevertheless, the great morphological variability of some species makes their identification and classification difficult. Therefore, the main aim of the present work was to assess the variability of the species of the Eumerus barbarus group in the western Mediterranean area under an integrative study (i.e., combining different techniques and data sources). We found high levels of morphological and genetic variability in two species of this group. Based on our findings, we described a new species from the island of Sardinia and provided the most comprehensive identification key for the males of this Eumerus species group from the western Mediterranean. Comprising nearly 300 described species, Eumerus Meigen, 1822, is one of the most speciose syrphid genera worldwide, and its taxonomic diversity is remarkable in the Mediterranean basin. The Eumerus barbarus (Coquebert, 1804) group consists of four species in the western Mediterranean. Although the phenotypic variability of this species group has been commented on in previous studies, it has never been contrasted with molecular data. In the present work, the morphological variation found in 300+ specimens of this species group from the western Mediterranean is explored and tested against the COI mitochondrial DNA (mtDNA). The highest phenotypic disparity was found in E. barbarus and Eumerus sulcitibius Rondani 1868. The integrative approach has not revealed cryptic diversity within the species E. barbarus but in E. sulcitibius. As a result, a new species close to E. sulcitibius was discovered, Eumerus sardus Aguado-Aranda, Ricarte & Hauser sp. n., from Sardinia, Italy. The new insular species is here described, illustrated, and discussed. A total of twenty-three haplotypes of COI mtDNA were identified amongst the analyzed Mediterranean specimens of E. barbarus, whereas two and five haplotypes were distinguished in the Iberian specimens of E. sulcitibius and Eumerus gibbosus van Steenis, Hauser & van Zuijen, 2017, respectively. Moreover, the first known barcodes of E. gibbosus and Eumerus schmideggeri van Steenis, Hauser & van Zuijen, 2017 were obtained, and the distribution ranges of all species are mapped. An updated dichotomous key to the males of the E. barbarus group from the western Mediterranean is provided. [ABSTRACT FROM AUTHOR]

Background Cleaning product use has been associated with adverse respiratory health effects such as asthma in cleaning staff and healthcare workers. Research in health effects from cleaning products has largely depended upon collecting exposure information by questionnaires which has limitations such as recall bias and underestimation of exposure. The aim of this study was to develop a Cleaning and Hazardous Products Exposure Logging (CHaPEL) app with a barcode scanner and to test the feasibility of this app with university cleaners. Methods The CHaPEL app was developed to collect information on demographics, individual product information, and exposure information. It also included an ease-of-use survey. A pilot study with university cleaning workers was undertaken in which cleaning workers scanned each product after use and answered the survey. Respiratory hazards of cleaning substances in the scanned cleaning products were screened by safety data sheets, a Quantitative Structure-Activity Relationship model and an asthmagen list established by an expert group in the US. Results Eighteen university cleaners participated in this study over a period of 5 weeks. In total, 77 survey responses and 6 cleaning products were collected and all reported that using the app was easy. The most frequently used product was a multi-surface cleaner followed by a disinfectant. Out of 14 substances in cleaning products, ethanolamine and Alkyl (C12-16) dimethyl benzyl ammonium chloride were found as respiratory hazardous substances. Conclusion The CHaPEL app is a user-friendly immediate way to successfully collect exposure information using the barcodes of cleaning products. This tool could be useful for future epidemiological studies focused on exposure assessment with less interruption to the workers. [ABSTRACT FROM AUTHOR]

In this study, we present a systematic investigation of the controlled fabrication of Au–Pd barcode nanowires within nanoporous anodic aluminum oxide (NP-AAO) templates. By using a combination of in situ X-ray diffraction (XRD), focused ion beam scanning electron microscopy (FIB-SEM), and transmission electron microscopy (TEM), we elucidate the influence of template preparation methods on the resulting nanowire properties. The template treatment, involving either pore widening or barrier layer thinning, significantly impacts nanowire growth. Through the analysis of the XRD data, we observe sequential deposition of Au and Pd segments with lattice parameter variations and strain effects. Particularly, the lattice parameters of Au and Pd segments display intricate temporal dependencies, influenced by interfacial effects and strain caused by growth under confinement. FIB-SEM imaging reveals uniform and reproducible nanowire lengths in the template treated with pore widening. Furthermore, TEM analysis confirms the presence of distinct Au and Pd segments, while scanning TEM–energy-dispersive X-ray spectroscopy revealed minor evidence of interdiffusion between the first and the second electrodeposited segments. Our findings emphasize the potential of the electrodeposition process within nanoporous templates for producing barcode nanowires with precise segmental properties. The combination of in situ XRD and electron microscopy offers valuable insights into the growth dynamics and structural characteristics of the fabricated Au–Pd barcode nanowires. This controlled fabrication strategy opens doors to tailoring nanowire properties for diverse applications, particularly in catalysis. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) are the largest class of receptors in the human genome and constitute about 30% of all drug targets. In this article, intended for a non-mathematical audience, both experimental observations and new theoretical results are compared in the context of information transmission across the cell membrane. The amount of information actually currently used or projected to be used in clinical settings is a small fraction of the information transmission capacity of the GPCR. This indicates that the number of yet undiscovered drug targets within GPCRs is much larger than what is currently known. Theoretical studies with some experimental validation indicate that localized heat deposition and dissipation are key to the identification of sites and mechanisms for drug action. [ABSTRACT FROM AUTHOR]

The Internet of Things (IoT) is a crucial component of the contemporary information industry and represents a significant advancement in information technology aimed at enhancing both human productivity and daily existence. Their applications are extensive and far-reaching. However, the present state of research on the design of low-cost IoT SoC chips leveraging open-source instruction set architectures lacks the requisite depth and breadth. To meet the requirements of low-cost IoT system-on-chip (SoC) development, this study presents a commodity code recognition SoC chip based on the RISC-V instruction set architecture, which is capable of performing image acquisition and barcode recognition. The proposed system comprises two main components: a low-power RISC-V processor and an image recognition module. This study initially enhanced the speed, accuracy, and area efficiency of the hardware design of a commodity barcode image-recognition module. Subsequently, the image recognition control module was developed using the RISC-V processor and CMOS image sensor OV7670, and the outcomes of image recognition were accessed through interrupts. The processing speed for collecting and identifying $640\times 480$ images on the FPGA board was 11.4FPS, and the image recognition rate was 99.5%. The chip was taped-out using the UMC55n process, which successfully decoded the barcodes and output the results at a working frequency of 40 MHz.

Nicaragua is a biodiverse country, but documented herpetological specimens are underrepresented compared to neighboring countries. In 2018 we conducted a collaborative expedition between the University of Michigan Museum of Zoology and Nicaraguan biologists. We visited sites in the Pacific Low‑ lands, Caribbean Lowlands, and the Central Highlands, representing the three major biogeographic regions of Nicaragua. We collected specimens of 100 species from a total of 106 encountered. We provide acces‑ sion numbers and morphological, genetic, and ecological information for these specimens. We recorded 23 new departmental records and the first country record of Metlapilcoatlus indomitus (Smith & Ferrari‑Castro, 2008), filling gaps in the known distribution of the species within Nicaragua and across Central America. When available for each species, we provide range maps and comparative genetic trees including conspecific reference sequences from the region, making this work a significant addition to existing checklists of the herpetofauna in Nicaragua.

The emergence of global health crises has emphasised the need for efficient and secure methods to verify the individuals’ vaccination and testing status. The research paper proposes an innovative application of the Radio Frequency Identification technology to develop a comprehensive system that ensures the controlled entry of vaccinated and tested individuals into buildings and extends its use to transportation networks. By combining tags, readers and a centralised database, with the extension of using Message Queuing Telemetry Transport, this solution aims to enhance public health safety, restore confidence in public spaces and optimise transportation operations.

For the first time, a simplified approach to constructing Bayesian neural networks is proposed, combining computational efficiency with the ability to analyze the learning process. The proposed approach is based on Bayesianization of a deterministic neural network by randomizing parameters only at the interface level, i.e., the formation of a Bayesian neural network based on a given network by replacing its parameters with probability distributions that have the parameters of the original model as the average value. Evaluations of the efficiency metrics of the neural network were obtained within the framework of the approach under consideration, and the Bayesian neural network constructed through variation inference were performed using topological data analysis methods. The Bayesianization procedure is implemented through graded variation of the randomization intensity. As an alternative, two neural networks with identical structure were used — deterministic and classical Bayesian networks. The input of the neural network was supplied with the original data of two datasets in versions without noise and with added Gaussian noise. The zero and first persistent homologies for the embeddings of the formed neural networks on each layer were calculated. To assess the quality of classification, the accuracy metric was used. It is shown that the barcodes for embeddings on each layer of the Bayesianized neural network in all four scenarios are between the corresponding barcodes of the deterministic and Bayesian neural networks for both zero and first persistent homologies. In this case, the deterministic neural network is the lower bound, and the Bayesian neural network is the upper bound. It is shown that the structure of data associations within a Bayesianized neural network is inherited from a deterministic model, but acquires the properties of a Bayesian one. It has been experimentally established that there is a relationship between the normalized persistent entropy calculated on neural network embeddings and the accuracy of the neural network. For predicting accuracy, the topology of embeddings on the middle layer of the neural network model turned out to be the most revealing. The proposed approach can be used to simplify the construction of a Bayesian neural network from an already trained deterministic neural network, which opens up the possibility of increasing the accuracy of an existing neural network without ensemble with additional classifiers. It becomes possible to proactively evaluate the effectiveness of the generated neural network on simplified data without running it on a real dataset, which reduces the resource intensity of its development.

CHO cells are most commonly used for the synthesis of recombinant proteins in biopharmaceutical production. When stable producer cell lines are obtained, the locus of transgene integration into the genome has a great influence on the level of its expression. Therefore, the identification of genomic loci ensuring a high level of protein production is very important. Here, we used the TRIP assay to study the influence of the local chromatin environment on the activity of transgenes in CHO cells. For this purpose, reporter constructs encoding eGFP under the control of four promoters were stably integrated into the genome of CHO cells using the piggyBac transposon. Each individual transgene contained a unique tag, a DNA barcode, and the resulting polyclonal cell population was cultured for almost a month without any selection. Next, using the high-throughput sequencing, genomic localizations of barcodes, as well as their abundances in the population and transcriptional activities were identified. In total, ~640 transgenes more or less evenly distributed across all chromosomes of CHO cells were characterized. More than half of the transgenes were completely silent. The most active transgenes were identified to be inserted in gene promoters and 5’ UTRs. Transgenes carrying Chinese hamster full-length promoter of the EF-1α gene showed the highest activity. Transgenes with a truncated version of the same promoter and with the mouse PGK gene promoter were on average 10 and 19 times less active, respectively. In total, combinations of genomic loci of CHO cells and transgene promoters that together provide different levels of transcriptional activity of the model reporter construct were described.

The monotypic genus Epithemis Laidlaw, 1955, is endemic to the Western Ghats and is represented by the nominate species Epithemis mariae (Laidlaw, 1915). Epithemis mariae is distributed across the Western Ghats, and as part of an ongoing study, we identified a distinct population from Wayanad. Morphological and molecular data for E. mariae and the population from the Wayanad plateau affirm that the two are distinct taxa and allow us to describe a new species. Epithemis wayanadensis sp. nov. is described based on male specimens collected from Wayanad, a part of the Western Ghats in Kerala state, southern India.

Silverfish (Zygentoma) are an ancient, but poorly studied group of primitively wingless insects. Species definition based on morphology alone is complicated by variations arising from the continuous moulting, even after reaching sexual maturity. In recent studies the use of molecular data has supported the identification of consistent morphological character traits, however only a small fraction of the species have been investigated. Eight species of the large silverfish genus Acrotelsella, collected by the first author from the Cape York Peninsula of northeastern Australia, are described and named as new species. Molecular data (COI and 28S) are presented that reinforces previous suggestions that the genus will eventually need to be split into two. [ABSTRACT FROM AUTHOR]

Astragalus is a crucial forage plant in the rangelands of northeastern Iran. However, identifying different species of Astragalus can be challenging due to their overlapping morphological features. In this study, we aimed to determine the relationships between 12 Astragalus species using both morphological and molecular traits. We also evaluated the effectiveness of DNA barcoding as a tool for identifying rangeland species of Astragalus in Northeast Iran. We examined five DNA barcodes, including three cpDNA regions (trnH-psbA, rpl32-trnL(UAG), and matK) and two nuclear sequences (ITS and ETS). We found that the plastid markers (rpl32-trnL(UAG, matK) were the most effective in differentiating between species. We also found that morphological data, as represented by the Neighbor-Net network and UPGMA dendrogram, had the potential to separate Astragalus species. We identified matK as the best and most accurate marker for barcoding, as trnH-psbA had some defects due to sequence size and alignment issues. Our study highlights the importance of using barcoding for quick and accurate recognition of plant species and shows the plastid markers were the most effective in differentiating between species. [ABSTRACT FROM AUTHOR]

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Despite the huge difference in land coverage between mountains and lowlands, most species are indeed found in mountains and foothills. The causes of this pattern have challenged biogeographers and evolutionary biologists. The Espinhaço and Mantiqueira Ranges are large mountain ranges from eastern Brazil that are global biodiversity hotspots located between the Brazilian Atlantic Forest (AF) and the Cerrado. However, Espinhaço and Mantiqueira species diversity may still be underestimated, either due taxonomic complexity or morphological cryptic species complexes. Two hylid frogs, Bokermannohyla nanuzae and Bokermannohyla feioi, are endemic, respectively, distributed in these two mountain ranges. These species were recently synonymized based on traditional taxonomy. We used data from the mitochondrial DNA (mtDNA) gene 16S and two nuclear genes to undertake phylogenetic and network, distance-based, and multispecies coalescent analyses on B. nanuzae, B. feioi, and an extensive outgroup dataset. We tested the monophyly of B. nanuzae, as well as the presence of candidate new species. Based on 16S phylogenetic analysis, We recovered B. nanuzae as paraphyletic, with B. sagarana nested within it. We recovered two main groups, with the geographic distribution generally corresponding to the Cerrado and AF boundaries. Probably due to ancestral polymorphism, both nuclear haplotype genealogies failed to distinguish B. nanuzae from the former B. feioi and/or from B. sagarana. The time-calibrated mtDNA tree revealed that B. martinsi, B. sagarana, and B. nanuzae have diverged during the Late Miocene, subsequently splitting into the remaining species/lineages during the Plio-Pleistocene. Taken together, our distance-based barcode and nuclear Bayesian analyses identified the former B. feioi, referred to as the AF group, as a distinct evolutionary lineage from B. nanuzae (Cerrado group). We provide the first insights into how different evolutionary lineages speciated in the highlands of southeastern Brazil and revalidated B. feioi for the AF group. [ABSTRACT FROM AUTHOR]

Russula subgenus Compactae is a group of ectomycorrhizal basidiomycetes, usually with large pileate fruitbodies. European members of the group are characterised by the absence of bright colours on the surfaces of their pilei, the context turning grey to black after cutting, the abundance of short lamellulae in the hymenophore, and spores with an inamyloid suprahilar spot and with low reticulate ornamentation. Our multi-locus phylogenetic study confirmed that this morphological delimitation corresponds to a well-supported clade. Within this clade, 16 species are recognised in Europe, of which five belong to the R. albonigra lineage and were described in a previous study, while eleven are fully described in this study. The application of the names R. acrifolia, R. adusta, R. anthracina, R. atramentosa, R. densissima, R. nigricans and R. roseonigra is based on the position of sequences retrieved from types or authentic material. Based on type sequences, R. fuliginosa is synonymised with R. anthracina and two varieties of R. anthracina are considered synonyms of R. atramentosa. The application of the name R. densifolia is based on a morphological match with the traditional species interpretation and the neotype specimen. Three species are described as new, R. marxmuelleriana sp. nov., R. picrophylla sp. nov. and R. thuringiaca sp. nov. This study recognises three major lineages and two species with isolated positions within the European Compactae and a morphological barcode was assigned to the species using an analysis of 23 selected characters. A search of publicly available sequences from the UNITE database revealed that the majority of species are host tree generalists and widely distributed in temperate and Mediterranean areas of Europe. Russula adusta is the only species so far proven to form ectomycorrhiza exclusively with conifers. [ABSTRACT FROM AUTHOR]

The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts. [ABSTRACT FROM AUTHOR]

Multiplex, rapid and accurate virus quantification plays a great value in biomedical detection. Here, a novel one step, wash-free immunoassay platform based bioinspired PhC barcodes for multiplexed virus quantification was explored. PhC barcodes were decorated with PDA by self-polymerization of DA, thus this nanocomposite hybridized PhC barcodes facilitated the adsorption of FITC labelled antibodies and quenched itself photoluminescent, allowing a fast responsive composite platform. In the presence of target analyte, the FITC-labelled detection antibody was released from the surface of PDA decorated microcarrier to specifically bind to the target analyte, thus recovered the photoluminescence. In addition, the PhC microcarrier was enabled to carry out various color barcode for different targets detection though tuning internal periodic structures. Based on these excellent performances of the nanocomposite barcode, this method can not only capture H1N1, H5N1, SARS-CoV-2 simultaneously with rapid, accuracy but also accomplish multiplex quantification detection with high-sensitivity. Furthermore, our developed platform was also achieved with high-sensitivity and high-specificity through the verification of clinical samples, thus laying out a new avenue for multiplex virus detection in clinical diagnosis.

The tropical dry forest is one of the world's most threatened ecosystems and is the habitat of the Robinson's Mouse Opossum (Marmosa robinsoni), a small marsupial within the Didelphidae family. This study aimed to describe cases of cuterebriases in free-ranging M. robinsoni by examining individuals caught in live animal traps. Sherman traps were deployed in four different sites over three different periods in five days. All animals passed through biometry, weighing, sampling parasites, and sampling feces. Only animals captured in the study site located close to the city were anesthetized and examined. The evaluation included blood samples and a clinical examination. Animals received anesthesia under physical restraint by intramuscular injections of ketamine and xylazine. For anesthetic reversion, the protocol was Yohimbine administered before release. In total, 8% (5/60) of all captured animals had fly larvae extracted from wounds. The molecular Barcode of the mitochondrial Cytochrome Oxidase I gene showed no match with any recognized species of Cuterebra. The animals weighed from 35 to 80 g and had lesions in the scapular region with parasites under their skin in sizes ranging from 1.3 to 2.2 cm. The animals with parasites were in good physical condition without evidence of disturbances in health conditions. This is compatible with literature, reporting little effect on population dynamics of other host species infected with Cuterebra larvae. The study included 24 animals captured in three areas far from any city, which showed no evidence of cuterebrid infection, suggesting that proximity to the city could increase exposure to cuterebriasis. There are reports of cuterebrids in M. robinsoni in Brazil; however, this is the first report of cuterebriasis in M. robinsoni in Colombia.

The multiple mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus have created variants with structural differences in both their spike and nucleocapsid proteins. While the functional relevance of these mutations is under continuous scrutiny, current findings have documented their detrimental impact in terms of affinity with host receptors, antibody resistance, and diagnostic sensitivity. Raman spectra collected on two British variant sub-types found in Japan (QK002 and QHN001) are compared with that of the original Japanese isolate (JPN/TY/WK-521), and found bold vibrational differences. These included: i) fractions of sulfur-containing amino acid rotamers, ii) hydrophobic interactions of tyrosine phenol ring, iii) apparent fractions of RNA purines and pyrimidines, and iv) protein secondary structures. Building upon molecular scale results and their statistical validations, the authors propose to represent virus variants with a barcode specially tailored on Raman spectrum. Raman spectroscopy enables fast identification of virus variants, while the Raman barcode facilitates electronic recordkeeping and translates molecular characteristics into information rapidly accessible by users.

Oral candidiasis, a common opportunistic infection of the oral cavity, is mainly caused by the following four Candida species (in decreasing incidence rate): Candida albicans, Candida glabrata, Candida tropicalis, and Candida krusei. This study offers in-depth Raman spectroscopy analyses of these species and proposes procedures for an accurate and rapid identification of oral yeast species. We first obtained average spectra for different Candida species and systematically analyzed them in order to decode structural differences among species at the molecular scale. Then, we searched for a statistical validation through a chemometric method based on principal component analysis (PCA). This method was found only partially capable to mechanistically distinguish among Candida species. We thus proposed a new Raman barcoding approach based on an algorithm that converts spectrally deconvoluted Raman sub-bands into barcodes. Barcode-assisted Raman analyses could enable on-site identification in nearly real-time, thus implementing preventive oral control, enabling prompt selection of the most effective drug, and increasing the probability to interrupt disease transmission.

Alternaria black spot of pomegranate (Punica granatum) was reported for the first time in Italy. In spring 2023, an outbreak of this disease was noticed in commercial pomegranate ‘Wonderful’ orchards of the municipality of Misterbianco (Sicily), following an unusually rainy period. A total of 30 randomly selected Alternaria isolates recovered from typical necrotic spots of leaves and fruits were characterized. Based on the colony morphology on solid agar media (PDA and MEA), isolates were separated into three distinct morphotypes (1, 2, and 3). The first two morphotypes comprised only isolates from fruits, while morphotype 3 comprised only isolates from leaves. Multigene phylogenetic analysis of four DNA regions, including internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a SCAR marker (OPA10–2), identified the isolates of morphotypes 1 and 2 as Alternaria alternata and morphotype 3 isolates as A. arborescens. In pathogenicity tests on unwounded leaves and fruit, the isolates of all three morphotypes produced symptoms on the leaves of three pomegranate cultivars, ‘Acco’, ‘Wonderful’, and ‘Etna’. The symptoms on ‘Acco’ leaves were the least severe. Conversely, the fruits of ‘Acco’ were the most susceptible. The isolates of morphotypes 2 and 3 were not pathogenic on the fruits of ‘Wonderful’ and ‘Etna’. This is the first report of Alternaria black spot in Italy and of A. arborescens associated with Alternaria black spot of pomegranate worldwide.

Abstract Background Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. Results We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. Conclusions MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.

In the department of Córdoba, 21 widely distributed Anopheles species have been described, of which Anopheles triannulatus, Anopheles nuneztovari, Anopheles albimanus, and Anopheles darlingi are the most abundant species, and the last three play a vectorial role in Malaria transmission in Colombia. A correct taxonomic identification of malaria insect vectors is of vital importance for the development of effective vector control strategies. However, the identification of individuals from the Anopheles genus presents difficulties due to the loss of relevant morphological characters during the transport and preservation of the collected specimens. In addition to the interspecific variations, and the intraspecific similarities of the species belonging to the subgenus Nyssorhynchus, since itpresents species complexes and cryptic species that difficults identification based only in morphological characteristics. The objective of this study was to characterize the barcode fragment of the COI gene and its genetic diversity for the identification of An. (Nys) nuneztovari and An. (Nys) albimanus in areas of high malaria transmission from the department of Córdoba. 67 individuals belonging to the species An. nuneztovari cytotype C and 22 An. albimanus were identified, and additionally, 9 haplotypes were obtained for An. nuneztovari C and 14 for An. albimanus distributed in the study areas. The values obtained in the FST and Nm estimators indicate a low or null genetic differentiation and a high gene flow between most of the studied populations because they share the most frequent haplotypes of these two species. The maximum likelihood trees for these species showed that the specimens from Córdoba belong to the same mitochondrial lineage as those previously reported from Antioquia, Choco, and Norte de Santander.

The use of global standards, and the placement of barcodes and data matrix codes on vaccine labels and other levels of packaging are crucial elements for the traceability of finished vaccine products. Vaccine manufacturers are committed to improving health through their products, as vaccine production offers opportunities that can be leveraged to benefit immunization systems. In 2019 the Developing Countries Vaccine Manufacturers Network (DCVMN) created the Supply Chain Initiative aimed at prioritize and explore traceability opportunities; concomitantly procurement agencies announced traceability requirements for vaccine global supply. Vaccine traceability brings benefits including supply chain reliability and safety through enhanced product movement visibility, and a reduction of falsified and expired vaccines circulating in the supply chain. DCVMN has coordinated the development and implementation of global traceability standards, at both primary and secondary vaccine packaging levels, to encourage and enable sharing these experiences. Six pilot studies in four different countries showed successful implementation, and constituted part of larger vaccine traceability work within the respective organizations. The main findings from these pilot studies indicated that stepwise approaches to the adoption of traceability standards allowed vaccine manufacturers to learn by doing, initially with lower risk, and to spread their investments over time. Because the value of traceability is in its scale of adoption and the use of the data, it remains important for all stakeholders to engage in and prioritize the journey of vaccine traceability, but also to suitably manage the financial risks. The DCVMN Supply Chain Initiative has demonstrated that its members are committed to driving supply system changes that benefit immunization, while recognizing that supply chain traceability is part of a larger healthcare ecosystem and should be adopted by countries and immunization programmes as well.

The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.

Olives (Olea europaea L.) are the most well-known trees of the Mediterranean basin. The genetic heritage of olive trees is very rich and characterized by an abundance of varieties, eventually leading to significant genotype mixing. Therefore, the classification and analysis of the genetic diversity of olive cultivars are challenges of high priority. It helps make more efficient use of the olive resources distributed globally and benefits the genetic improvement and breeding of olive varieties. DNA barcoding is a method for evaluating and classifying species that uses short, variable, and uniform DNA regions. This study used DNA sequencing data for the first time for DNA barcoding of Egyptian olive cultivars and assessed the genetic relationship between four local cultivars grown in Egypt and their relation to sequences within the database. PCR amplification and sequence characterization were used to assess the effectiveness of the two barcoding sites, rbcL and matK. Based on multiple alignments of all the sequences obtained from the analyzed regions, matK had the longest sequence (816 bp) and rbcL the shortest (411 bp) of the two barcoding loci. The matK gene region was the least varied, with a variability level of 77%, while the rbcL gene region had the highest amount of variability (98.7%). Because of the presence of unique variable sites, both barcoding loci rbcL and matK efficiencies discriminate the selective Egyptian olive cultivars. The DNA sequences from the individual and combined barcode loci were used in a maximum likelihood tree-based phylogenetic analysis to successfully distinguish the selected olive cultivars. [ABSTRACT FROM AUTHOR]

The larvae of the genus Chironomus are a common object for hydrobiological studies, as well as a model object for cytogenetics. Morphologically, the species are very similar. One of these species or species complex is Chironomus "annularius", which has a Holarctic distribution. It has chromosomal banding sequences characteristic of Nearctic and Palearctic populations. Using an integrated method that included morphology, cytogenetics, and molecular genetics, we analyzed populations from Russia, Mongolia, and Armenia. We found through cytogenetics and larval morphology that the populations have high similarity. Molecular genetic studies have shown significant differences between the populations. The genetic distances between the populations, in some cases, exceed the interspecific threshold of 3%, and are 6.5%. In the South Caucasian population (Lake Sevan), a chromosomal banding sequence, h'annD3, that was previously observed only in North America, was found for the first time. The larvae from Lake Sevan have large genetic distances from others, and are morphologically similar to the species Chironomus markosjani Shilova 1983, described from this lake without comparison with Ch. annularius nor an exact description of the karyotype. The sequences of the COI genes from Montenegro (Lake Skadar) and West Siberia (Novosibirsk) found in GenBank may belong to a new undescribed species, or a species not represented in the database. Thus, the analyzed data on Chironomus "annularius" support the presence of the complex of homosequential species under this name. [ABSTRACT FROM AUTHOR]

The tropical dry forest is one of the world's most threatened ecosystems and is the habitat of the Robinson's Mouse Opossum (Marmosa robinsoni), a small marsupial within the Didelphidae family. This study aimed to describe cases of cuterebriases in free-ranging M. robinsoni by examining individuals caught in live animal traps. Sherman traps were deployed in four different sites over three different periods in five days. All animals passed through biometry, weighing, sampling parasites, and sampling feces. Only animals captured in the study site located close to the city were anesthetized and examined. The evaluation included blood samples and a clinical examination. Animals received anesthesia under physical restraint by intramuscular injections of ketamine and xylazine. For anesthetic reversion, the protocol was Yohimbine administered before release. In total, 8% (5/60) of all captured animals had fly larvae extracted from wounds. The molecular Barcode of the mitochondrial Cytochrome Oxidase I gene showed no match with any recognized species of Cuterebra. The animals weighed from 35 to 80 g and had lesions in the scapular region with parasites under their skin in sizes ranging from 1.3 to 2.2 cm. The animals with parasites were in good physical condition without evidence of disturbances in health conditions. This is compatible with literature, reporting little effect on population dynamics of other host species infected with Cuterebra larvae. The study included 24 animals captured in three areas far from any city, which showed no evidence of cuterebrid infection, suggesting that proximity to the city could increase exposure to cuterebriasis. There are reports of cuterebrids in M. robinsoni in Brazil; however, this is the first report of cuterebriasis in M. robinsoni in Colombia. [Display omitted] • In total, 14% (5/36) of the animals captured within Barranquilla had cuterebrid bot fly larvae extracted from wounds. • The COX1 gene sequences matched Cuterebra sp. (JQ246700) with similarities between 94.8% and 94.9%. • The taxonomic assignment could not be made to the species level. • Results raise the hypothesis that the proximity to the city could affect the prevalence of cuterebriasis in this species. [ABSTRACT FROM AUTHOR]