Expertise In Biology Research Articles

CRCI2NA inaugural symposium: A meeting on tumor and immune ecosystems.

The CRCI2NA inaugural symposium, a meeting on tumor and immune ecosystems, took place in the vibrant and picturesque city of Nantes. The meeting gathered world-renowned experts in cancer biology and immunology. It showcased the most advanced science on mechanisms driving cellular heterogeneity, plasticity, and signaling in normal and cancer cellular ecosystems, which contribute to cancer development, progression, and therapeutic resistance. Recent developments in cancer immunotherapy and anti-tumor strategies were also discussed to collectively assess new therapeutic vulnerabilities to defeat cancer.

From wild to captive: Understanding the main nutritional diseases of sharks in public aquariums.

The establishment of a well-adapted and accurate feeding regimen is a fundamental determining factor in the maintenance of shark species in captivity. Replicating the natural diet in captivity is commonly accepted and recommended. Given the diverse nutritional composition of prey, supplementation may become necessary. The captive environment poses unique challenges, making sharks susceptible to an array of health issues, including numerous diseases. Mitigating these risks demands detailed husbandry practices, an appropriate physical environment and a balanced diet. Supplementation, encompassing vitamins and minerals, becomes imperative for the provision of essential nutrients. This complexity has rendered the formulation of an adapted feeding plan for aquarists exceptionally challenging. The scarcity of information in these species adds to the issue, mandating extrapolation from various shark groups and to species with analogous characteristics. This literature review concentrates predominantly on benthic and pelagic shark species prevalent in contemporary aquariums. The central argument posits that dietary choices in captivity rely on factors such as availability, quality and consistency of supply. The advocated approach highlights the importance of a balanced, diverse feeding that closely mirrors natural diets. It is then crucial to emphasize that these are general guidelines, and the specific dietary requisites may diverge between shark species. Collaborating with experts in marine biology, shark husbandry and veterinary care is imperative for the formulation and perpetuation of an adapted diet for captive sharks.

Measuring carbohydrate recognition profile of lectins on live cells using liquid glycan array (LiGA).

Glycans constitute a significant fraction of biomolecular diversity on cellular surfaces across all kingdoms of life. As the structure of glycans is not directly encoded by the organism's DNA, it is impossible to use high-throughput DNA technologies to study the role of cellular glycosylation or to understand how glycocalyx is recognized by glycan-binding proteins (GBPs). To address this gap, we recently described a liquid glycan array (LiGA) platform that allows profiling of glycan-GBP interactions on the surface of live cells in vitro and in vivo using next-generation sequencing. LiGA is a library of DNA-barcoded bacteriophages, where each clonal bacteriophage displays 5-1,500 copies of a glycan and the distinct DNA barcode inside each bacteriophage clone encodes the structure and density of the displayed glycans. Deep sequencing of the glycophages associated with live cells yields a glycan-binding profile of GBPs expressed on the surface of cells. This protocol provides detailed instructions for how to use LiGA to probe cell surface receptors and includes information on the preparation of glycophages, analysis by MALDI-TOF mass spectrometry, the assembly of a LiGA library and its deep sequencing. Using this protocol, we measure glycan-binding profiles of the immunomodulatory sialic acid-binding immunoglobulin-like lectins‑1, -2, -6, -7 and -9 expressed on the surface of different cell types. Compared with existing methods that require complex specialist equipment, this method allows users with basic molecular biology expertise to measure the precise glycan-binding profile of GBPs on the surface of any cell type expressing exogenous GBP within 2-3 d.

Cell scientist to watch – Gokul Upadhyayula

ABSTRACT Srigokul (Gokul) Upadhyayula is Scientific Director of the Advanced BioImaging Center (ABC) and an Assistant Professor in Residence of Cell Biology, Development and Physiology at the University of California (UC), Berkeley, USA. Gokul completed his PhD in the bioengineering department with Valentine Vullev at UC Riverside, where he built his first microscope. Inspired to apply his fascination with microscopy and image analysis to understanding biological phenomena, he subsequently joined the group of Tomas Kirchhausen at Harvard Medical School as a postdoc and collaborated with Eric Betzig at Janelia Research Campus on major advances in adaptive optical lattice light-sheet microscopy (LLSM) technology to study fundamental cellular processes such as clathrin-mediated endocytosis and nuclear pore reformation. In 2019, he moved to UC Berkeley to build the ABC together with Eric Betzig. The ABC aims to enhance the accessibility and adoption of data-heavy imaging technologies like LLSM. Gokul's team combines expertise in biology, chemistry, engineering, microscopy and computational science to provide resources and tools that allow biologists to extract meaningful insights from imaging data. We spoke with Gokul over Zoom to learn about his career path, the challenges that come with handling massive bioimaging datasets and the vision of the ABC for the future of bioimaging.

Cell scientist to watch – Virginie Hamel

ABSTRACT Virginie Hamel is a co-Group Leader and Senior Lecturer in the Department of Molecular and Cellular Biology at the University of Geneva (UNIGE) in Switzerland. She completed her PhD with Iain Mattaj at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, studying nuclear envelope re-assembly. To gain experience with bioimaging, she joined Pierre Gönczy's laboratory at the Swiss Institute for Experimental Cancer Research (ISREC) in Lausanne as a postdoc and later became a Staff Scientist. There, she began researching centriole assembly, combining biochemical approaches and super-resolution microscopy with expertise in structural biology from her partner in the lab and in life, Paul Guichard. In 2015, Virginie and Paul started their joint Centriolar Architecture lab at UNIGE, focusing on the structural cell biology of centrioles. Their development of advanced expansion microscopy (ExM) methods has helped unravel the roles of centriolar proteins in human disease and visualise cytoskeletal organisation in diverse eukaryotic cells. For our Special Issue on Imaging Cell Architecture and Dynamics, we spoke with Virginie over Zoom about her career, the benefits of running a joint lab with her partner, and the exciting advances being made with techniques like ExM.

Interdisciplinarity through internationality: Results from a US-Mexico graduate course bridging computational and plant science.

Interdisciplinarity is used to integrate and synthesize new research directions between scientific domains, but it is not the only means by which to generate novelty by bringing diverse perspectives together. Internationality draws upon cultural and linguistic diversity that can potentially impact interdisciplinarity as well. We created an interdisciplinary class originally intended to bridge computational and plant science that eventually became international in scope, including students from the United States and Mexico. We administered a survey over 4 years designed to evaluate student expertise. The first year of the survey included only US students and demonstrated that biology and computational student groups have distinct expertise but can learn the skills of the other group over the course of a semester. Modeling of survey responses shows that biological and computational science expertise is equally distributed between US and Mexico student groups, but that nonetheless, these groups can be predicted based on survey responses due to subspecialization within each domain. Unlike interdisciplinarity, differences arising from internationality are mostly static and do not change with educational intervention and include unique skills such as working across languages. We end by discussing a distinct form of interdisciplinarity that arises through internationality and the implications of globalizing research and education efforts.

Collaborative learning in the digital age: empowering tuberculosis researchers through virtual training.

Integrating whole genome sequencing (WGS) of the Mycobacterium tuberculosis complex into routine care, surveillance, and research in high tuberculosis burden settings remains challenging due to limited resources and skills. While technological platforms for scaling WGS are emerging, scaling wet lab and analytic components often depends on partnerships where such skills have been established. To address this, a virtual training program was developed. Over 12 weeks, 21 trainees from five Southern African institutes engaged in learning from curated theoretical content and interactive virtual meetings with experienced instructors. The training program, developed by a diverse team of experts in molecular biology, biomedical research, microbiology, and tuberculosis research, provided comprehensive coverage aligned with the latest advancements. Teaching strategies included interactive mentor-led sessions and real-time feedback, together with facilitated knowledge exchange and understanding. The virtual training program yielded several successes. Of note, trainees submitted three scientific articles for peer review, based on their acquired knowledge and its application in research. The program also fostered collaborations on Mycobacterium tuberculosis WGS among participants, showcasing the potential for networking and future joint projects. While the virtual training program encountered challenges related to the pandemic, limited resources, trainee engagement, and language barriers, these were creatively mitigated. To improve future training sessions, a platform assessing participant engagement and information retention is recommended. Wider collaborative efforts among experts and institutions in collating resources will lead to more comprehensive training programs. Addressing challenges such as internet connectivity issues and language barriers is crucial for ensuring inclusivity and enhancing the overall learning experience. In conclusion, the virtual training program successfully provided knowledge and skill training in WGS to trainees, leading to scientific article submissions and collaborations. Furthermore, content creators benefited from improved science communication and training opportunities.

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants.

The ClinGen Hereditary Breast, Ovarian, and Pancreatic Cancer (HBOP) Variant Curation Expert Panel (VCEP) is composed of internationally recognized experts in clinical genetics, molecular biology, and variant interpretation. This VCEP made specifications for the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) guidelines for the ataxia telangiectasia mutated (ATM) gene according to the ClinGen protocol. These gene-specific rules for ATM were modified from the ACMG/AMP guidelines and were tested against 33 ATM variants of various types and classifications in a pilot curation phase. The pilot revealed a majority agreement between the HBOP VCEP classifications and the ClinVar-deposited classifications. Six pilot variants had conflicting interpretations in ClinVar, and re-evaluation with the VCEP's ATM-specific rules resulted in four that were classified as benign, one as likely pathogenic, and one as a variant of uncertain significance (VUS) by the VCEP, improving the certainty of interpretations in the public domain. Overall, 28 of the 33 pilot variants were not VUS, leading to an 85% classification rate. The ClinGen-approved, modified rules demonstrated value for improved interpretation of variants in ATM.

Photodynamic therapy with NIR-II probes: review on state-of-the-art tools and strategies.

In 2022 10% of the world's population was aged 65+, and by 2100 this segment is expected to hit 25%. These demographic changes place considerable pressure over healthcare systems worldwide, which results in an urgent need for accurate, inexpensive and non-invasive ways to treat cancers, a family of diseases correlated with age. Among the therapeutic tools that gained important attention in this context, photodynamic therapies (PDT), which use photosensitizers to produce cytotoxic substances for selectively destroying tumor cells and tissues under light irradiation, profile as important players for next-generation nanomedicine. However, the development of clinical applications is progressing at slow pace, due to still pending bottlenecks, such as the limited tissue penetration of the excitation light, and insufficient targeting performance of the therapeutic probes to fully avoid damage to normal cells and tissues. The penetration depth of long-wavelength near infrared (NIR) light is significantly higher than that of short-wavelength UV and visible light, and thus NIR light in the second window (NIR-II) is acknowledged as the preferred phototherapeutic means for eliminating deep-seated tumors, given the higher maximum permissible exposure, reduced phototoxicity and low autofluorescence, among others. Upon collective multidisciplinary efforts of experts in materials science, medicine and biology, multifunctional NIR-II inorganic or organic photosensitizers have been widely developed. This review overviews the current state-of-the art on NIR-II-activated photosensitizers and their applications for the treatment of deep tumors. We also place focus on recent efforts that combine NIR-II activated PDT with other complementary therapeutic routes such as photothermal therapy, chemotherapy, immunotherapy, starvation, and gas therapies. Finally, we discuss still pending challenges and problems of PDT and provide a series of perspectives that we find useful for further extending the state-of-the art on NIR-II-triggered PDT.

The Alliance Between the German Cancer Research Center and Bayer: A Retrospective of an Innovative Collaboration Model.

In 2009, the German Cancer Research Center (DKFZ) and the biopharmaceutical company Bayer AG initiated an academic-industry co-discovery collaboration. The partners combined their expertise in tumor biology and drug discovery to identify and validate novel targets for cancer treatment. In the early phase of the Alliance, the focus was on target identification and validation projects. Over time, both partners realized that they could also successfully collaborate on later stages of drug discovery. As a result over the past few years, and following several contract extensions, the two partners have collaborated on several late-stage drug discovery projects. This has resulted in the achievement of several drug discovery milestones and the initiation of early clinical trials, the most recent in 2022. This success has been possible thanks to both partners' understanding of each other's needs and challenges. They jointly developed solutions to issues such as the intrinsic potential conflict of early publishing versus patent protection. Both partners also appreciated the risks involved in some of the experiments, such as starting a joint laboratory for immune-therapy with scientists from both parties working bench-to-bench. Recently, despite these successes the partners decided to terminate the Alliance, as Bayer AG wants to focus its activities on the development of its late pipeline.

Sosialisasi Bahaya Narkotika sebagai Bentuk Kenakalan Remaja di kalangan Siswa SMKN 1 Kecamatan Kragilan Kabupaten Serang

Narcotics are a substance that is very dangerous if its use is misused and permission is not obtained from the authorities, narcotics will damage the nation's next generation who will run the government in the future. The rise in the use of narcotics is in line with the influx of globalization and modernization which makes it easier for people to obtain them as well as a network of dealers who are aggressively looking for marketing targets among young people who are susceptible to sweet advances and do not yet have clear life principles. Indonesia is one of the countries that is fighting drug dealers, users and networks, this is because every 17 seconds someone is arrested for violating drug-related laws. Indonesia has 2 laws that regulate the misuse of narcotics, namely Law No. 35 of 2009 and Law No. 5 of 1997. All of them are clear about the sanctions and dangers of using narcotics, the punishment can even be death. This service journal refers to biological theory which explains the biological theory of the brain, metabolic imbalance theory, and genetic theory. Many experts, especially biological experts, say that narcotics will damage brain growth and development. This service journal uses literature and seminar methods which are expected to provide an explanation of a situation where an individual or person will have a bleak future if they fall into the use of narcotics because it will damage brain tissue and damage the body. As early as possible, we will unite together to fight against narcotics, not only for law officers who work, but all elements of society are involved in fighting the use of narcotics which has penetrated young people, especially among teenagers who are still at school, who are vulnerable to the temptation of using narcotics.

A new flow path: eDNA connecting hydrology and biology

AbstractEnvironmental DNA (eDNA) has revolutionized ecological research, particularly for biodiversity assessment in various environments, most notably aquatic media. Environmental DNA analysis allows for non‐invasive and rapid species detection across multiple taxonomic groups within a single sample, making it especially useful for identifying rare or invasive species. Due to dynamic hydrological processes, eDNA samples from running waters may represent biodiversity from broad contributing areas, which is convenient from a biomonitoring perspective but also challenging, as hydrological knowledge is required for meaningful biological interpretation. Hydrologists could also benefit from eDNA to address unsolved questions, particularly concerning water movement through catchments. While naturally occurring abiotic tracers have advanced our understanding of water age distribution in catchments, for example, current geochemical tracers cannot fully elucidate the timing and flow paths of water through landscapes. Conversely, biological tracers, owing to their immense diversity and interactions with the environment, could offer more detailed information on the sources and flow paths of water to the stream. The informational capacity of eDNA as a tracer, however, is determined by the ability to interpret the complex biological heterogeneity at a study site, which arguably requires both biological and hydrological expertise. As eDNA data has become increasingly available as part of biomonitoring campaigns, we argue that accompanying eDNA surveys with hydrological observations could enhance our understanding of both biological and hydrological processes; we identify opportunities, challenges, and needs for further interdisciplinary collaboration; and we highlight eDNA's potential as a bridge between hydrology and biology, which could foster both domains.This article is categorized under: Science of Water > Hydrological Processes Science of Water > Methods Water and Life > Nature of Freshwater Ecosystems

Extraordinary model systems for regeneration.

Regeneration is the remarkable phenomenon through which an organism can regrow lost or damaged parts with fully functional replacements, including complex anatomical structures, such as limbs. In 2019, Development launched its 'Model systems for regeneration' collection, a series of articles introducing some of the most popular model organisms for studying regeneration in vivo. To expand this topic further, this Perspective conveys the voices of five expert biologists from the field of regenerative biology, each of whom showcases some less well-known, but equally extraordinary, species for studying regeneration.

EU’s Medical Device Expert Panels: Analysis of Membership and Published Clinical Evaluation Consultation Procedure (CECP) Results

BackgroundThe new EU Medical Device Regulation (MDR) places greater importance on the role of clinical evidence to establish safety and performance. Article 54 of the MDR calls for expert committees to independently review the scientific, technical, and clinical evidence supporting the market authorization of certain novel devices independently from the established process of Notified Body reviews. These experts provide a review and opinion that ultimately is taken into consideration alongside the information reviewed by the Notified Body during the review process. Four expert committees (General and Plastic Surgery and Dentistry; Orthopaedics, Traumatology, Rehabilitation, Rheumatology; Circulatory System; and Neurology) have published at least one Scientific Opinion (SO) under the Clinical Evaluation Consultation Procedure (CECP) in 2021–2022.MethodsThe four expert committees with published CECP opinions were reviewed to assess the academic backgrounds and professional expertise of each member with respect to clinical, technical, and biological domains on a 0–2 scale for each domain. A content review was conducted on the 10 CECP opinions published by these committees to assess their consistency with the goals and outcome expectations set by the MDR. The extent of content related to each of the clinical, technical, and biological domains was also assessed on a 0–2 scale.ResultsAll committees were composed primarily by members with strong clinical expertise, but only a few had strong technical and biological expertise. Across committees, the average scores of members related to academic background and professional expertise both ranged from 1.64 to 2.00 in the clinical domain, but only 0–0.15 and 0.15–0.69, respectively, in the biological domain, and 0.12–0.55 and 0.23–0.73, respectively, in the technical domain. A content review for the 10 SOs showed that all opinions focused exclusively or primarily on the clinical evidence. Three contained a modest amount of additional text directed at technical/engineering issues and five at biological issues.ConclusionExpert committees are composed predominantly of expert clinical reviewers but have many fewer members with significant technical or biological expertise. This may limit the ability of the committees to evaluate the significant technical and biological risks that are often best understood by preclinical testing. Broadening the expertise across the committees may improve the depth of their benefit/risk critiques.

Robotics Autonomous Systems (RAS) in Food Laboratories are the Future of Food Processing Industries: A Review

Recent advancements in robotics have witnessed significant progress in both industrial and mobile robotics, paving the way for a new era of automation. However, a paradigm shift is underway in robotics research, focusing on enhancing the interaction between humans and robots, termed as service robotics. This emerging field aims to cater to a wide array of human social needs by bridging the gap between man and machine. Traditionally, laboratory automation has been constrained by the rigid control mechanisms of computer-driven robots. Despite their utility, particularly in liquid handling tasks, many laboratory procedures remain only partially automated. Nonetheless, by breaking down laboratory processes into discrete unit operations and integrating them, overarching analysis schemes can be accomplished. The future of laboratory automation necessitates interdisciplinary skills, requiring scientists to blend biological knowledge with engineering expertise to fully exploit its potential. Simultaneously, a new wave of robotic innovations is permeating various sectors, from robot lawn mowers to autonomous vehicles, alongside smarter robots in manufacturing environments. This progression underscores the increasing reliance on automation, with future research endeavours expected to pivot towards leveraging laboratory automation to tackle novel scientific challenges. This abstract underscore the necessity for future scientists to acquire a comprehensive skill set that integrates both biological knowledge and engineering expertise. It highlights the trend towards greater automation in laboratory environments, representing the merging of scientific and engineering fields to tackle new research challenges.

New Insights on Molecular Autopsy in Sudden Death: A Systematic Review.

Sudden unexpected deaths often remain unresolved despite forensic examination, posing challenges for pathologists. Molecular autopsy, through genetic testing, can reveal hidden causes undetectable by standard methods. This review assesses the role of molecular autopsy in clarifying SUD cases, examining its methodology, utility, and effectiveness in autopsy practice. This systematic review followed PRISMA guidelines and was registered with PROSPERO (registration number: CRD42024499832). Searches on PubMed, Scopus, and Web of Science identified English studies (2018-2023) on molecular autopsy in sudden death cases. Data from selected studies were recorded and filtered based on inclusion/exclusion criteria. Descriptive statistics analyzed the study scope, tissue usage, publication countries, and journals. A total of 1759 publications from the past 5 years were found, with 30 duplicates excluded. After detailed consideration, 1645 publications were also excluded, leaving 84 full-text articles for selection. Out of these, 37 full-text articles were chosen for analysis. Different study types were analyzed. Mutations were identified in 17 studies, totaling 47 mutations. Molecular investigations are essential when standard exams fall short in determining sudden death causes. Expertise in molecular biology is crucial due to diverse genetic conditions. Discrepancies in post-mortem protocols affect the validity of results, making standardization necessary. Multidisciplinary approaches and the analysis of different tissue types are vital.

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants.

The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP) Variant Curation Expert Panel (VCEP) is composed of internationally recognized experts in clinical genetics, molecular biology and variant interpretation. This VCEP made specifications for ACMG/AMP guidelines for the ataxia telangiectasia mutated (ATM) gene according to the Food and Drug Administration (FDA)-approved ClinGen protocol. These gene-specific rules for ATM were modified from the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) guidelines and were tested against 33 ATM variants of various types and classifications in a pilot curation phase. The pilot revealed a majority agreement between the HBOP VCEP classifications and the ClinVar-deposited classifications. Six pilot variants had conflicting interpretations in ClinVar and reevaluation with the VCEP's ATM-specific rules resulted in four that were classified as benign, one as likely pathogenic and one as a variant of uncertain significance (VUS) by the VCEP, improving the certainty of interpretations in the public domain. Overall, 28 the 33 pilot variants were not VUS leading to an 85% classification rate. The ClinGen-approved, modified rules demonstrated value for improved interpretation of variants in ATM.

X-LoRA: Mixture of low-rank adapter experts, a flexible framework for large language models with applications in protein mechanics and molecular design

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, our gating strategy uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations to solve tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities, including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics, and design. The impact of this work includes access to readily expandable and adaptable models with strong domain knowledge and the capability to integrate across areas of knowledge. Featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, protein biophysics, mechanics, and quantum-mechanics based molecular properties, we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, adversarial agentic modeling including ontological knowledge graph construction, and molecular design. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins or quantum mechanical molecular properties but also reasoning over the results and correctly predicting likely mechanisms that explain distinct molecular behaviors.

Are Biology Experts and Novices Function Pluralists?

Are Biology Experts and Novices Function Pluralists?

Developing a Common Global Baseline for Nucleic Acid Synthesis Screening.

Nucleic acid synthesis is a powerful tool that has revolutionized the life sciences. However, the misuse of synthetic nucleic acids could pose a serious threat to public health and safety. There is a need for international standards for nucleic acid synthesis screening to help prevent the misuse of this technology. We outline current barriers to the adoption of screening, which include the cost of developing screening tools and resources, adapting to existing commercial practices, internationalizing screening, and adapting screening to benchtop nucleic acid synthesis devices. To address these challenges, we then introduce the Common Mechanism for DNA Synthesis Screening, which was developed in consultation with a technical consortium of experts in DNA synthesis, synthetic biology, biosecurity, and policy, with the aim of addressing current barriers. The Common Mechanism software uses a variety of methods to identify sequences of concern, identify taxonomic best matches to regulated pathogens, and identify benign genes that can be cleared for synthesis. Finally, we describe outstanding challenges in the development of screening practices. The Common Mechanism is a step toward ensuring the safe and responsible use of synthetic nucleic acids. It provides a baseline capability that overcomes challenges to nucleic acid synthesis screening and provides a solution for broader international adoption of screening practices. The Common Mechanism is a valuable tool for preventing the misuse of synthetic nucleic acids. It is a critical step toward ensuring the safe and responsible use of this powerful technology.