Life Sciences Research Articles

Multiplex Digital Nucleic Acid Analysis by a LAMP-Argonaute Coupling Assay via a Parallel Droplet Fusion SlipChip.

Multiplex digital nucleic acid analysis (NAA) allows the precise quantification of multiple target nucleic acids with single-molecule sensitivity, making it highly appealing for life science research and clinical diagnostics. Nucleic acid-guided endonucleases, such as CRISPR, have demonstrated great potential in digital NAA. However, performing multiplex digital NAA with an endonuclease remains challenging. The thermophilic Argonaute protein (Ago) enables specific targeting of multiple sequences by a single enzyme, exhibiting superior potential in multiplex detection. Here, we developed a multiplex digital NAA by coupling nucleic acid amplification and Ago-specific detection using parallel droplet fusion facilitated by a SlipChip. The SlipChip can generate a series of droplets to perform multiplex digital loop-mediated isothermal amplification (LAMP), followed by a series of droplets containing Ago reagents for parallel mixing and reactions, resulting in three distinct digital fluorescence signals (FAM, ROX, and Cy5) corresponding to each specific target sequence. We performed viral load analysis of respiratory viruses, including influenza A, influenza B, and SARS-CoV-2, within 60 min. In addition, we used this digital LAMP-Ago assay to analyze viral loads in 34 clinical samples. The system provides a multiplex digital NAA capable of precise nucleic acid quantification with high sensitivity and specificity.

Going down the rabbit hole: insight into the future of Paramecium (Ciliophora, Protista) biodiversity surveys

Paramecium, a research subject in many areas of life sciences, appeared to be a ciliate genus with a well known biodiversity structure. However, the understanding of its biological diversity has been evolving rapidly in recent years, driven by the discovery of new taxa and an expanded knowledge of the distribution of known species. Most future insights into Paramecium biodiversity are expected to come from molecular data, particularly through eDNA sampling. As one of the most recognisable microeukaryotes, commonly found in freshwater ecosystems, and with over a century of biodiversity research – including extensive reference data from GenBank records and living culture collections – Paramecium holds significant potential to become a model ciliate for studies in biodiversity and biogeography. This review addresses the challenges of species identification within the Paramecium genus, the current state of knowledge on its biodiversity and other factors that may shape future research. Despite some existing bottlenecks, new approaches to data acquisition and analysis will enable researchers to integrate diverse lines of evidence, allowing for exceptional explorations of Paramecium species and populations.

The changing world dynamics of research performance

AbstractIn recent years, a notable diversification in the geographical representation of the World’s top universities could be observed. Chinese universities play an increasingly prominent role in these rankings, thus indicating that we might be in the midst of a regional shift in academic performance. To explore this dynamics, we analyze seven years’ worth of data used for university rankings by academic subjects from the Academic Ranking of World Universities (ARWU). We focus on China, Europe, the USA, and other global regions of the world. We find that China has indeed seen an unprecedented growth in Engineering and Life Sciences research, positioning itself rather firmly as a leader in these fields. Conversely, the USA leads in the Social Sciences, while Europe excels in Geography, Ecology, Public and Business Administration, and Pharmacy. Other regions worldwide stand out in Transportation Science, Nursing, and Hospitality & Tourism Management. These results reveal the evolving landscape of global academic research, highlighting regional strengths and emerging world trends in subject-specific excellence.

수시 개정 교육과정기 실과 검정 교과서 농업 생명과학 영역 단원의 체제 비교분석

This study analyzes the system and content of the agricultural life science unit in the practical textbook developed during the occasional revised curriculum. It seeks to provide implications and recommend improvement measures for the development of future textbooks. The study’s findings lead to several recommendations. First, the average proportion (15.4%) of the actual science textbooks in the agricultural life science field during the revised curriculum period is considered to be somewhat lower than the status of the actual science as the parent study. Therefore, future textbooks should increase both the quality and quantity of agricultural life science education content. Second, besides knowledge acquisition, the agricultural life science unit should emphasize attitude formation, practical application, and execution. Since current practical textbooks focus on knowledge-oriented learning goals, there is a need to harmonize knowledge, attitudes, and skills in future revisions. Third, auxiliary data and experiential activities of the agricultural life science unit of the periodically revised curriculum should presented in a balanced manner without any bias. Fourth, it is desirable for unit evaluation items in the agricultural life science field to harmonize 'convergence type evaluation' and 'divergence type evaluation'. Fifth, this study examined the system of units in the agricultural life science field across all practical science textbooks developed during curriculum revisions. Future research should examine changes in the content, including the 2022 revised textbook, and analyze differences in content organization across textbooks.

Third time’s the charm: nomenclatural availability provided to the nomina of two Bornean Cyrtodactylus (Squamata, Gekkonidae)

Davis et al. (2023a) published the descriptions of two new Bornean species of the highly speciose gekkonid genus Cyrtodactylus Gray, 1827 in the journal Zoologica Scripta. The descriptions themselves actually appeared in the online supplementary information to this paper as Appendix S1, accessible as a link under “Supporting Information” on the Wiley Online Library page associated with the paper’s DOI. Life Science Identifiers (LSIDs) for ZooBank registration entries for the new nomina were provided in this Appendix but were not given in the body of the main paper, which was published electronically on 1 February 2023. As noted by Davis et al. (2023b), however, the Appendix is a separate document from the main paper and it exists only in an editable Word format, not in a fixed PDF/A format, and as such, the conditions of Article 8.1.3.2 of the amended Code (Anonymous 2012), that nomenclatural acts be available as “widely accessible electronic copies with fixed content and layout”, were not met. Because of this lack of ZooBank registration in the online version of the paper, it cannot be considered as validly promulgated, nor can the nomina therein (Article 8, as amended in 2012). The subsequent publication of the print version of the manuscript in the May 2023 issue of Zoologica Scripta (actual date of publication not stated) did meet the criteria for the promulgation of the nomina C. kapitensis and C. hutan, but did not meet the requirement of Article 13.1.1 that “a new nomen published after 1930 must be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon”, as the diagnostic and descriptive data supporting the recognition of these two taxa were present only in the ephemeral Appendix S1, leaving these nomina nomenclaturally unavailable. This situation is illustrative of some of the numerous previously identified problems with the inclusion of nomenclatural acts in online supplements (see also Dubois et al. 2013, 2022).

Syrian refugee youths' science learning in a “dialogic” third space: Pushing boundaries in the Lebanese educational system through translanguaging

AbstractThe purpose of this study was to explore translanguaging space as a transformative third space, where alternative and competing discourses are celebrated and where science learning and the development of science's discourse and epistemic practices expand across overlapping boundaries (e.g., home, school, and community). The study focused on Syrian refugee youth adapting to learning science in English in the Lebanese multilingual educational system that esteems international languages (English or French) over Arabic. Our research questions included: (1) What translanguaging practices and functions emerge during a linguistically responsive life science unit designed for refugee multilingual learners? (2) How does a translanguaging space act as a third space for refugee learners to engage in meaning‐making and science practices and discourse around the topic of “respiration”? The study utilized a qualitative instrumental case‐study approach to generate data around refugee learners' languaging practices and their development of science understandings, practices, and discourse. We also engaged in participatory methodologies that challenge boundaries between researchers and participants. The data sources were 22 Zoom recordings, students' work, and participant‐generated feedback. Thematic analysis was used to analyze transcripts and students' work while adhering to trustworthiness criteria. Our findings center translanguaging as a justice‐oriented pedagogy that enables a productive and “inviting” third space for refugee multilingual learners to make meaning of phenomena by bringing together and extending their semiotic and epistemic repertoires. Serving multi‐tiered functions, translanguaging fostered dialogic connections that affirmed students' “outside” social spaces as valuable resources for meaning‐making in science classrooms. The implications discuss design features that support a fluid and purposeful translanguaging third space for asset‐oriented science learning.

EXTRACURRICULAR SCIENTIFIC ACTIVITIES OF STUDENTS IN A PEDAGOGICAL UNIVERSITY

The article is devoted to the study of the peculiarities of the organization and development of extracurricular scientific activity (ESA) of students at the Herzen State Pedagogical University of Russia (HSPUR). The idea of the importance of ESA in the preparation of future teachers is substantiated in connection with the increasing demands on the quality of training of teaching staff, the compliance of the higher education system with the challenges of modern times and the need to strengthen the role of scientific activity in the educational process. Based on the analysis of data collected during an in-depth interview, in which leading specialists from various structural divisions of the university who supervise the extracurricular scientific activity of students took part, the mechanisms and forms of organization of ESA at HSPUR are revealed. The main attention is paid to the functioning of student scientific societies (SSS), which are key elements of the system of extracurricular scientific initiatives. It is emphasized that SSS have a flexible structure and are the most successful form of student self-government, allowing to combine individual scientific interests of students with the tasks of the educational program. The article provides a detailed description of the main functions of the Student Scientific Society, such as developing students' research competencies, supporting scientific events and assisting in the publication of scientific papers. The problems that arise in the process of organizing the Student Scientific Society are discussed, including low motivation of a significant portion of students and a lack of resources for conducting full-fledged scientific research. The article presents proposals for improving the organization and development of ESA. Among them, measures are highlighted to attract students to the scientific life of the university from their first years, increase the attractiveness of scientific research activities, support and improve the incentive system, as well as create conditions for the effective functioning of the institutional infrastructure of student science.

Interpretation of SuratAl-Qadr by Sheikh Ahmad bin Muhammad Al-Suhaimi (deceased in 1178 AH) from his statement: "And a specific night is committed" from page (5) to page (7), up to his saying: "If they revive it; they would be most worthy of being called 'worshippers'" -Study and Verification

In this research, I discussed two aspects: The first chapter: The author's personal and scientific life, by explaining: his name, lineage, title, birth, upbringing, death, students, mentors, and his writings.The second part of the research, I dedicated to the verified text, where I explained the author's interpretation of Surah Al-Qadr, and the virtue of reviving this great night due to its great reward. As God Almighty says: "The Night of Decree is better than a thousand months" (1). The author explained the interpretation of this noble verse, when this blessed night occurs during the nights of Ramadan, its signs, the great reward for those who revive this blessed night, the recommended supplication to be said during it, and the reason for the revelation of this blessed surah.

Memoirs of a researcher as a literary fact (based on V. Ivanov’s memoirs about the East)

The article examines the memoirs of Vladimir Alekseevich Ivanov (1886–1970), a prominent Russian orientalist, the founder of Ismaili studies, a branch of Islamic studies that explores Ismailism as a religious and ideological movement within the Shiite branch of Islam. Written in the mid-1960s, these memoirs cover the period from 1918 to 1968 and convey the researcher’s impressions of the Eastern countries he visited (Central Asia, Iran, Iraq, India, Egypt, Syria and Palestine). The handwritten notes of the scientist are kept in the archival collection of the Institute of Oriental Manuscripts of the Russian Academy of Sciences (Moscow, St. Petersburg). In 2015, they were published as a separate book with a preface and comments by B. Norik, a Russian Iranian scholar, translator, textual critic, employee of the Institute of Oriental Studies of the Russian Academy of Sciences (Moscow). The memoirs of V. Ivanov have so far been studied as a fact of his scientific life and fate, as a certain addition to the researcher’s work, a kind of appendix to them, explaining what usually lies beyond strict studies, in the field of subjective experience and impressions. Meanwhile, it seems that they represent a completely independent literary work, so that the circle of their readers cannot be limited only to narrow specialists. The literary part of the memoirs is determined by a whole set of features: its language (style register), the image of the author and his subjective position, genre features of the work combining elements of diary prose and detective story, as well as a conditionally “hagiographic” canon (ancient Russian literature) with the traditions of ethnographic descriptions of everyday life, which dates back to “Walking across Three Seas” by Afanasy Nikitin. The memoirist, as a rule, records the past selectively (this is due not only to the conscious desire of the author to highlight some events, obscuring others, but also to the specifics of human memory as such). V. Ivanov was no exception, for him of primary nature was the opinion taken from the point of view of the interests of science.

A stable combination of non-stable genes outperforms standard reference genes for RT-qPCR data normalization

Gene expression profiling is of key importance in all domains of life sciences, as medicine, environment, and plants, for both basic and applied research. Despite the emergence of microarrays and high-throughput sequencing, qPCR remains a standard method for gene expression analyses, with its data normalization step being crucial for ensuring accuracy. Currently, the most widely used normalization method is based on the use of reference genes, assumed to be stably expressed across all experimental conditions. In the present study, we show that finding a stable combination of genes, regardless of their individual stability, outperforms standard reference genes for RT-qPCR data normalization. A stable combination of genes consists of a fixed number of genes whose individual expression balance each other all along experimental conditions of interest. Moreover, the present study shows that such an optimal combination of genes can be found using a comprehensive database of RNA-Seq data. Indeed, assuming that such a comprehensive database contains accurate gene expression profiles, we can extract in silico, by the way of the mathematical variance calculation, a stable combination of genes that reflects in vivo stability. As a case study, this new method was developed using the tomato model plant, with corresponding RNA-Seq data from the TomExpress database. However, the method is potentially applicable to other organisms with available RNA-seq data. Our results demonstrate the superiority of the reported method over commonly used housekeeping genes or other stably expressed genes. We therefore recommend the use of our new method together with classic ones in order to always obtain the best reference genes for a given experimental design.

Snowflake Data Warehouse for Large-Scale and Diverse Biological Data Management and Analysis.

With the increasing speed of genomic, transcriptomic, and metagenomic data generation driven by the advancement and widespread adoption of next-generation sequencing technologies, the management and analysis of large-scale, diverse data in the fields of life science and biotechnology have become critical challenges. In this paper, we thoroughly discuss the use of cloud data warehouses to address these challenges. Specifically, we propose a data management and analysis framework using Snowflake, a SaaS-based data platform. We further demonstrate its convenience and effectiveness through concrete examples, such as disease variant analysis and in silico drug discovery. By introducing Snowflake, researchers can efficiently manage and analyze a wide array of biological data, enabling the discovery of new biological insights through integrated analysis. Through these specific methodologies and application examples, we aim to accelerate research progress in the field of bioinformatics.

Assessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine).

The National Library of Medicine (NLM) currently indexes close to a million articles each year pertaining to more than 5300 medicine and life sciences journals. Of these, a significant number of articles contain critical information about the structure, genetics, and function of genes and proteins in normal and disease states. These articles are identified by the NLM curators, and a manual link is created between these articles and the corresponding gene records at the NCBI Gene database. Thus, the information is interconnected with all the NLM resources, services which bring considerable value to life sciences. National Library of Medicine aims to provide timely access to all metadata, and this necessitates that the article indexing scales to the volume of the published literature. On the other hand, although automatic information extraction methods have been shown to achieve accurate results in biomedical text mining research, it remains difficult to evaluate them on established pipelines and integrate them within the daily workflows. Here, we demonstrate how our machine learning model, GNorm2, which achieved state-of-the art performance on identifying genes and their corresponding species at the same time handling innate textual ambiguities, could be integrated with the established daily workflow at the NLM and evaluated for its performance in this new environment. We worked with 8 biomedical curator experts and evaluated the integration using these parameters: (1) gene identification accuracy, (2) interannotator agreement with and without GNorm2, (3) GNorm2 potential bias, and (4) indexing consistency and efficiency. We identified key interface changes that significantly helped the curators to maximize the GNorm2 benefit, and further improved the GNorm2 algorithm to cover 135 species of genes including viral and bacterial genes, based on the biocurator expert survey. GNorm2 is currently in the process of being fully integrated into the regular curator's workflow.

MULTILINGUAL EDUCATION IN LIFE SCIENCES: TEACHERS' AND LEARNERS' BELIEFS ABOUT CODE-SWITCHING

In South Africa, where multilingualism is prevalent, code-switching—a practice of alternating between languages—plays a significant role in shaping classroom dynamics and learning outcomes. This study explores the beliefs of both teachers and learners regarding code-switching in Life Sciences classrooms. Utilizing quantitative methods, the research is grounded in the Cognitive Academic Language Proficiency (CALP) framework which emphasizes the pivotal role of language in the learning process. Data were collected from 100 learners and 44 secondary school teachers across multilingual areas in Sedibeng West, Gauteng Province in South Africa, using questionnaires. The findings reveal that teachers view code-switching as an effective strategy for clarifying complex scientific concepts and addressing language barriers, despite concerns about its potential impact on language proficiency and dependency. Learners, on the other hand, value code-switching for its role in making learning material more accessible and understandable. This study highlights the nuanced role of code-switching in enhancing educational outcomes in multilingual settings and suggests its potential benefits and challenges in the context of Life Sciences education. Keywords: cognitive academic language proficiency, code-switching, learner beliefs, multilingual education, teacher beliefs

Evaluation of the Anti-Psoriatic Activity of Mangifera Indica Flower Extract in Different Solvents

Mangifera indica (M.indica) is considered to be medicinal plant that belongs to ayurvedic family of plants used against numerous diseases and disorders. The objective of this research is to assess the anti-psoriatic effectiveness M.indica flower extract in various solvents. The current study was designed to formulate an anti-psoriatic spray at Fatima Tul Zahra Department of Life Sciences, Muhammad Institute of Medical & Allied Science, Multan. The M.indica flowers were collected from Multan Mango Farm and M.indica flowers extracts were prepared separately by macerated grinding of fresh flowers using different solvents (n-hexane, ethanol and olive oil) by mortar and pestle that were stored in air tight glass bottles separately for 7days before filtration through double layered muslin cloth. The filtrate (pellets) were obtained from filtered pharmaceutical product through rotary evaporator at 37°C at low pressure to prepare 5%, 10% and 20% (W/V) solutions with same solvents separately that were applied topically using sprayer bottles on psoriasis affected skin area of rabbits to evaluate the therapeutic effects keeping the patients free of any other allopathic medicines for two week. Out of 33 rabbits with mean age 34.62±5.11 years, 27 rabbits were trialed in experimental group (n=27), other than positive control (n=3) and negative control (n=3), while corticosteroid ointment and distilled water were used as standard drug for positive control and negative control groups respectively. Surprisingly in our study, 100% rabbits were recovered from psoriasis treated with olive oil flowers extract that was 33.33% of experimental group. Statistical analysis was done with SPSS version-22, based on obtained data during research trial. Lack of proper treatment and adverse effects of allopathic medicines including anticancer drugs urged the way to find the natural products with anti-psoriatic activity. The present findings suggest that the M.indica flowers extract possesses significant potential in mitigating psoriasis-related symptoms. The diverse solvents used for extraction demonstrated variations in efficacy, emphasizing the importance of solvent selection in extracting bioactive compounds.

A practical, biomimetic, one-pot synthesis of firefly luciferin.

The bioluminescence reaction of firefly luciferase with D-luciferin has become an indispensable imaging technique in modern biology and life science experiments, but the high cost of D-luciferin is limiting its further application. Here, we report a practical, one-pot synthesis of D-luciferin from p-benzoquinone (p-BQ), L-cysteine methyl ester and D-cysteine, with an overall yield of 46%. Our route, which is six steps in length and proceeds via 2-cyano-6-hydroxybenzothiazole, is inspired by the mechanistic study of our previously reported biomimetic, non-enzymatic, one-pot formation of L-luciferin from p-BQ and L-cysteine. Advantages of our route include its high yield, low cost, use of only inexpensive, commercially available reagents, without requiring strictly anhydrous and oxygen-free conditions, and elevated temperatures.

Preface: 2024 International Conference on Biomedicine, Food Science and Public Health (BFSPH 2024)

We are proud to organize the 2024 International Conference on Biomedicine, Food Science and Public Health (BFSPH 2024), which was held in Manchester, United Kingdom from December 21-22, 2024. This conference brings together innovative scholars and experts in the fields of biomedicine, cell biology, food science, life sciences, and public health to a common forum. The main purpose of the conference is to promote research and development activities. Another goal is to promote the exchange of information among researchers, developers, experts, students, and practitioners worldwide. These multi-faceted disciplines are converging very fast. We would like to deeply acknowledge all the parties involved in making BFSPH 2024 successfully held. Besides, we wish to thank all authors and participants for providing their valuable contributions for this proceeding as well as the reviewers for their constructive recommendations and criticism aiding to improve the presented papers. With best regards, BFSPH Conference Organizing Committees Manchester, United Kingdom

Precision Nutrient and Soil Tillage Management for Sustainable Winter Barley Production (Hordeum vulgare L.) and Tillage Impact on Soil CO2 Emission

Precision sustainable agronomic practices are crucial for achieving global food security as well as mitigating climate change. A field experiment was conducted at the Hungarian University of Agriculture and Life Sciences in Gödöllő from 2023 to 2024. The study aimed to evaluate the effects of soil tillage and foliar nutrient supplementation on winter barley yield, associated characteristics, and soil CO2 emissions. Employing a split-plot design with three replications, the experiment included four nutrient treatments (control, bio-cereal, bio-algae, and MgSMnZn blend) and two soil tillage type (i.e., plowing and cultivator). The study found that soil CO2 emissions were influenced by the crop growth stage across both tillage treatments throughout the growing seasons, but the tillage system itself did not have an effect. Similarly, the leaf chlorophyll content was not affected by tillage and nutrient treatments. Plant height, the leaf area index (LAI), and thousand kernel weights (TKW) were significantly affected by nutrient treatments across the growing seasons. Both nutrient and tillage treatments also had a notable effect on the number of productive tillers in winter barley. Moreover, nutrient and tillage treatments consistently influenced grain yield across the two growing seasons, and their interaction significantly impacted both grain yield and thousand kernel weights. The bio-cereal nutrient treatment combined with plowing tillage yielded the highest values for most parameters throughout the growing seasons. Therefore, it can be concluded that the combination of bio-cereal nutrient treatments and plowing tillage can boost winter barley yields. Notably, soil CO2 emissions peak during the crops’ reproductive stage, surpassing levels from early growth.

Methodological exploration of using gene editing technology to study gene function and disease mechanism

This paper discusses the application of gene editing technology, especially CRISPR-Cas9 system, in the study of gene function and disease mechanism. By modifying the genome sequence at a fixed point, gene editing technology uses specific nucleases to induce double strand breaks, trigger DNA repair mechanism, and realize accurate gene modification. This paper introduces the working principle of CRISPR-Cas9 and its application in establishing gene knock-out and knock-in models, and emphasizes the importance of this technology in revealing gene function and molecular mechanism of diseases. However, gene editing technology also faces challenges such as off-target effect and technical accuracy, and involves ethical issues. Therefore, the article puts forward that we should strengthen ethical review, improve laws and regulations, and enhance public awareness. In a word, gene editing technology provides a powerful tool for life science and medical research, and shows a broad application prospect.

A beginner’s guide to design of experiments for life sciences using Spreadsheet DoE

Life science research frequently involves optimizing experimental conditions to maximize product yield, ensuring the research pipeline can progress efficiently. For instance, in biochemistry, many processes in the protein production and characterization pipeline need optimizing such as cloning, protein expression, protein purification, and a range of structural biology techniques and functional assays. Design of Experiments (DoE) is an approach that designs a set of experiments that varies all factors at the same time for rapid process optimization, however, this approach presents a challenge due to statistical complexities and high software costs. To address this, DoE is introduced with Spreadsheet DoE, an open access user-friendly educational factorial design tool that provides step-by-step guidance and transparent spreadsheet calculations. Protein expression optimization in Escherichia coli is used as an example, and other biochemical optimizations are also explored. This guide along with Spreadsheet DoE aims to encourage researchers with minimal statistical background to effectively employ DoE methodologies in their life science studies.

Protein-metabolite Interactions Based on Chemical Targeting Methods.

The importance of the protein-metabolite interaction network extends beyond its relevance to life sciences focused on proteins, it also profoundly influences its mechanisms related to disease targets, drug screening, and clinical diagnosis and treatment. Research methods targeting protein-metabolite interaction focus on enhancing the detectable signals of specific interactions by examining the structural characteristics of both proteins and metabolites in conjunction with chemical molecules, playing a crucial role in elucidating the protein-metabolite interaction network. Consequently, this article outlines several chemical targeting strategies developed in recent years and provides examples of their applications in the discovery and interpretation of new protein-metabolite interaction pathways. Finally, a brief summary will be presented regarding technological advances, research prospects, and current challenges of protein-metabolite interaction research.