From Animaculum to single molecules: 300 years of the light microscope

Evolution of the ocular immune system

The evolution of the ocular immune system should be viewed within the context of the evolution of the immune system, and indeed organisms, as a whole. Since the earliest time, the most primitive responses of single cell organisms involved molecules such as anti-microbial peptides and behaviours such as phagocytosis. Innate immunity took shape ~2.5 billion years ago while adaptive immunity and antigen specificity appeared with vertebrate evolution ~ 500 million years ago. The invention of the microscope and the germ theory of disease precipitated debate on cellular versus humoral immunity, resolved by the discovery of B and T cells. Most recently, our understanding of the microbiome and consideration of the host existing symbiotically with trillions of microbial genes (the holobiont), suggests that the immune system is a sensor of homoeostasis rather than simply a responder to pathogens. Each tissue type in multicellular organisms, such as vertebrates, has a customised response to immune challenge, with powerful reactions most evident in barrier tissues such as the skin and gut mucosa, while the eye and brain occupy the opposite extreme where responses are attenuated. The experimental background which historically led to the concept of immune privilege is discussed in this review; however, we propose that the ocular immune response should not be viewed as unique but simply an example of how the tissues variably respond in nature, more or less to the same challenge (or danger).

Imaging malaria parasites across scales and time

The idea that disease is caused at the cellular level is so fundamental to us that we might forget the critical role microscopy played in generating and developing this insight. Visually identifying diseased or infected cells lays the foundation for any effort to curb human pathology. Since the discovery of the Plasmodium-infected red blood cells, which cause malaria, microscopy has undergone an impressive development now literally resolving individual molecules. This review explores the expansive field of light microscopy, focusing on its application to malaria research. Imaging technologies have transformed our understanding of biological systems, yet navigating the complex and ever-growing landscape of techniques can be daunting. This review offers a guide for researchers, especially those working on malaria, by providing historical context as well as practical advice on selecting the right imaging approach. The review advocates an integrated methodology that prioritises the research question while considering key factors like sample preparation, fluorophore choice, imaging modality, and data analysis. In addition to presenting seminal studies and innovative applications of microscopy, the review highlights a broad range of topics, from traditional techniques like white light microscopy to advanced methods such as superresolution microscopy and time-lapse imaging. It addresses the emerging challenges of microscopy, including phototoxicity and trade-offs in resolution and speed, and offers insights into future technologies that might impact malaria research. This review offers a mix of historical perspective, technological progress, and practical guidance that appeal to novice and advanced microscopists alike. It aims to inspire malaria researchers to explore imaging techniques that could enrich their studies, thus advancing the field through enhanced visual exploration of the parasite across scales and time.

Molecular markers in cell cycle visualisation during development and stress conditions in Arabidopsis thaliana

Plant growth and development are tightly regulated by cell division, elongation, and differentiation. A visible plant phenotype at the tissue or organ level is coordinated at the cellular level. Among these cellular regulations (cell division, elongation and differentiation), cell division in plants follows the same universal mechanisms across kingdoms of life, and involves conserved cell cycle regulatory proteins (cyclins, cyclin-dependent kinase and cell cycle inhibitors). Cell division is regulated through distinct cell cycle steps (G1, S, G2 and M), and these individual steps are visualised using transgenic marker lines. As a result, a quantitative cell cycle approach in plants during development and stress conditions relies on the accuracy of cell cycle markers. In this perspective article, we highlight the available cell cycle marker lines in plants, common practices within plant biology communities based on existing literature and provide a road map to a thorough quantitative approach of cell cycle regulation in plants.

Automated discovery of experimental designs in super-resolution microscopy with XLuminA

Driven by human ingenuity and creativity, the discovery of super-resolution techniques, which circumvent the classical diffraction limit of light, represent a leap in optical microscopy. However, the vast space encompassing all possible experimental configurations suggests that some powerful concepts and techniques might have not been discovered yet, and might never be with a human-driven direct design approach. Thus, AI-based exploration techniques could provide enormous benefit, by exploring this space in a fast, unbiased way. We introduce XLuminA, an open-source computational framework developed using JAX, a high-performance computing library in Python. XLuminA offers enhanced computational speed enabled by JAX's accelerated linear algebra compiler (XLA), just-in-time compilation, and its seamlessly integrated automatic vectorization, automatic differentiation capabilities and GPU compatibility. XLuminA demonstrates a speed-up of 4 orders of magnitude compared to well-established numerical optimization methods. We showcase XLuminA's potential by re-discovering three foundational experiments in advanced microscopy, and identifying an unseen experimental blueprint featuring sub-diffraction imaging capabilities. This work constitutes an important step in AI-driven scientific discovery of new concepts in optics and advanced microscopy.

Hematological cytomorphology: Where we are

The manuscript discusses the historical evolution of observing blood cell morphology under an optical microscope, from the earliest microscopes in the 17th century to the modern digital era, highlighting key advancements and contributions in the field. Blood has historically held symbolic importance in various cultures, with early medical observations dating back to Hippocrates and Galeno. The discovery of cells and subsequent advancements in microscopy by scientists like Hooke and van Leeuwenhoek paved the way for understanding blood cell morphology. Influential figures such as Hewson, Donné, and Ehrlich followed. Diagnostic cytology evolved from manual cell counting to the development of automated hematological systems. Automated complete blood counting came to support microscopic examination in diagnosing hematological disorders. Morphology is crucial in predicting disease outcomes and guiding treatment decisions, particularly hematological neoplasms. The introduction of flow cytometry and its integration with traditional morphological analysis and the new cytogenetic and molecular techniques revolutionized the classification and prognostication of hematologic disorders. Digital microscopy has emerged as a powerful tool in recent years, offering rapid acquisition and sharing of blood cell images. Integrating Artificial Intelligence with digital microscopy has further enhanced morphological analysis, improving diagnostic efficiency. We also discuss the prospects of AI in pre-classifying blood cells in bone marrow aspirate samples, potentially revolutionizing diagnostic pathways for hematologic diseases. Overall, the manuscript provides a comprehensive overview of the historical development, clinical significance and technological advancements in observing blood cell morphology, underscoring its continued relevance in modern hematology practice.

Examining the fabric of the eye: Antoni van Leeuwenhoek, the draper and ocular microscopist

We review Antoni van Leeuwenhoek's (1632 - 1723) microscopic studies of comparative ocular anatomy in humans, mammals, birds, and fish. His contributions in anatomical microscopy to ocular biology has been overshadowed by his prolific work and first observations of protists and bacteria, spermatozoa, red blood cells, and dental plaque. Leeuwenhoek's Delftian optical and artisanal heritage more than compensated for any lack of formal scientific training and, in keeping with his Royal Society ethos, shone light onto the "fabric of the eye" in order to better understand its function, which he had extended with his microscopes. He has provided the earliest known microscopic descriptions of the tear film, eyelids, cornea, aqueous, crystalline lens, vitreous, retina, optic nerve, and photoreceptor--as well as the first descriptions of cataract, vitreous floaters, and corneal pathology. His description of the aquatic mammal Cetacean eye foreshadowed an understanding of the optical complexities of aerial and submarine vision of whales. His observations challenged classical teaching at that time, particularly in relation to the optic nerve.

Five historical innovations that have shaped modern otolaryngological surgery

Throughout history, many innovations have contributed to the development of modern otolaryngological surgery, improving patient outcomes and expanding the range of treatment options available to patients. This article explores five key historical innovations that have shaped modern otolaryngological surgery: Operative Microscope, Hopkins Rigid Endoscope, Laryngeal Nerve monitoring, Cochlear implants and Laser surgery. The selection of innovations for inclusion in this article was meticulously determined through expert consensus and an extensive literature review. We will review the development, impact and significance of each innovation, highlighting their contributions to the field of otolaryngological surgery and their ongoing relevance in contemporary and perioperative practice.

Igniting children's enthusiasm for microbes with an origami paper microscope

The COVID-19 pandemic has underscored the urgent need for microbiology literacy in society. Microbiology knowledge, and its dissemination, can help inform and increase the objectivity of important decisions, such as treatment or vaccination. A microbiology learning experience titled "What you can't see can hurt you" was delivered as part of a larger outreach event where children were exposed to various aspects of medicine and health care fields. The activity involved an introduction to and a discussion of bacteria of clinical importance and the use of a smartphone-attachable paper-based foldable microscope. To explore the impact of this activity on participants' interest in science and microbiology, a pre- and post-activity survey of five questions on an emoji-based Likert scale was completed by the participants. A statistically significant increase in their interest in microbes and where to find them, as well as in microscopy, was observed after the event. Making microbes visible to children and allowing them to capture images of microbes exposes them directly and personally to microscopy and microbiology. An affordable low-cost paper-based microscope can become an alternative approach to teaching and learning to deliver clinical microbiology information to a wide audience range.

If it's a target, it's a pan-cancer target: Tissue is not the issue

Cancer is traditionally diagnosed and treated on the basis of its organ of origin (e.g., lung or colon cancer). However, organ-of-origin diagnostics does not reveal the underlying oncogenic drivers. Fortunately, molecular diagnostics have advanced at a breathtaking pace, and it is increasingly apparent that cancer is a disease of the genome. Hence, we now have multiple genomic biomarker-based, tissue-agnostic Food and Drug Administration approvals for both gene- and immune-targeted therapies (larotrectinib/entrectinib, for NTRK fusions; selpercatinib, RET fusions; dabrafenib plus trametinib, BRAFV600E mutations; pembrolizumab/dostarlimab, microsatellite instability; and pembrolizumab for high tumor mutational burden; pemigatinib is also approved for FGFR1-rearranged myeloid/lymphoid neoplasms). There are emerging targets as well, including but not limited to ALK, BRCA and/or homologous repair deficiency, ERBB2 (HER2), IDH1/2, KIT, KRASG12C, NRG1, and VHL. Many tissue-agnostic approvals center on rare/ultra-rare biomarkers (often < 1 % of cancers), necessitating screening hundreds of tumors to find a single one harboring the cognate molecular alteration. Approval has generally been based on small single-arm studies (<30-100 patients) with high response rates (>30 % to > 75 %) of remarkable durability. Because of biomarker rarity, single-gene testing is not practical; next generation sequencing of hundreds of genes must be performed to obtain timely answers. Resistance to biomarker-driven therapeutics is often due to secondary mutations or co-driver gene defects; studies are now addressing the need for customized drug combinations matched to the complex molecular alteration portfolio in each tumor. Future investigation should expand tissue-agnostic therapeutics to encompass both hematologic and solid malignancies and include biomarkers beyond those that are DNA-based.

Complement and MHC patterns can provide the diagnostic framework for inflammatory neuromuscular diseases

Histopathological analysis stands as the gold standard for the identification and differentiation of inflammatory neuromuscular diseases. These disorders continue to constitute a diagnostic challenge due to their clinical heterogeneity, rarity and overlapping features. To establish standardized protocols for the diagnosis of inflammatory neuromuscular diseases, the development of cost-effective and widely applicable tools is crucial, especially in settings constrained by limited resources. The focus of this review is to emphasize the diagnostic value of major histocompatibility complex (MHC) and complement patterns in the immunohistochemical analysis of these diseases. We explore the immunological background of MHC and complement signatures that characterize inflammatory features, with a specific focus on idiopathic inflammatory myopathies. With this approach, we aim to provide a diagnostic algorithm that may improve and simplify the diagnostic workup based on a limited panel of stainings. Our approach acknowledges the current limitations in the field of inflammatory neuromuscular diseases, particularly the scarcity of large-scale, prospective studies that validate the diagnostic potential of these markers. Further efforts are needed to establish a consensus on the diagnostic protocol to effectively distinguish these diseases.

[Methods for assessing the microbiological diversity of the ocular surface]

This review compares data from scientific studies on the microbial community of the ocular surface (OS) in conditionally healthy individuals using cultural methods (including culture-dependent diagnostic tests), microscopic and molecular genetic methods, and assesses the influence of research methods and sample preparation on the results. Concordance and discordance of the sets of identified microorganisms were analyzed using overlapping and non-overlapping methods of studying the microbial community of a healthy OS. The article presents tables showing the names of microorganisms that were identified in different sources. Cross-verification in taxa of different ranks helped confirm the following most frequently found microorganisms on healthy OS: coccomorphic microorganisms of the genera Staphylococcus, Micrococcus, Kocuria, Streptococcus, Enterococcus; gram-positive spore-forming bacilli of the genera Bacillus and Paenibacillus; gram-positive non-spore-forming rod-shaped bacteria, including Corynebacterium, but excluding Propionibacterium and Microbacterium; gram-negative non-spore-forming rod-shaped microorganisms of the genera Moraxella and Serratia. The study also assessed the effect of wearing soft contact lenses on the composition of the microbial community of the OS.

Lessons learned from the successful polio vaccine experience not learned or applied with the development and implementation of the COVID-19 vaccines

The eradication of polio during the latter half of the 20th century can be considered one of the greatest medical triumphs in history. This achievement can be attributed to the development of vaccines that received the public's almost unwavering acceptance of them, especially by parents who had been waiting/hoping for a medical breakthrough that would ensure that their children would not succumb to the devastating effects of infantile paralysis. Sixty years later, the worldwide population was now confronted with an equally devastating disease - Covid-19 - which by the 2020-2021 time period had reached pandemic levels not seen since the flu outbreak of 1918. Unlike polio, however, several vaccines against Covid-19 were rapidly developed and deployed due to advances in microbiologic and immunologic technology. But also, unlike the polio vaccine experience, there was not universal acceptance of the Covid-19 vaccines and this has led to continuation of the pandemic into 2023 (albeit at a reduced level). In addition, acceptance of the Covid-19 vaccines has been confronted with the uncertainty that they do not apparently prevent transmission in asymptomatic people, and the mutation rate of the virus requires periodic re-evaluation and possible upgrading of the vaccines. This review will focus on the various factors that have led to these contrasting attitudes toward these two different vaccines and how resistance and hesitancy to vaccine use can be overcome by implementing various measures, after introducing the key roles that the sciences of microbiology and immunology have played in vaccine development over the past 250+ years.

Evolution of operating microscopes and development of 3D visualization systems for intraocular surgery

The recent development of high-resolution, heads-up, 3D visualization microscopy systems has provided new technical and visualization options for ophthalmic surgeons. In this review, we explore the evolution of microscope technologies, the science behind modern 3D visualization microscopy systems, and the practical benefits (as well as disadvantages) that these systems provide over conventional microscopes for intraocular surgical practice. Overall, modern 3D visualization systems reduce the requirements for artificial illumination and provide enhanced visualization and resolution of ocular structures, improving ergonomics, and facilitating a superior educational experience. Even when considering their disadvantages, such as those related to technical feasibility, 3D visualization systems have an overall positive benefit/risk ratio. It is hoped these systems will be adopted into routine clinical practice, pending further clinical evidence on the benefits they may provide on clinical outcomes.

Modern tools applied to classic structures: Approaches for mammalian male germ cell RNA granule research

First reported in the 1800s, germ cell granules are small nonmembrane bound RNA-rich regions of the cytoplasm. These sites of critical RNA processing and storage in the male germ cell are essential for proper differentiation and development and are present in a wide range of species from Caenorhabditis elegans through mammals. Initially characterized by light and electron microscopy, more modern techniques such as immunofluorescence and genetic models have played a major role in expanding our understanding of the composition of these structures. While these methods have given light to potential granule functions, much work remains to be done. The current expansion of imaging technologies and omics-scale analyses to germ cell granule research will drive the field forward considerably. Many of these methods, both current and upcoming, have considerable caveats and limitations that necessitate a holistic approach to the study of germ granules. By combining and balancing different techniques, the field is poised to elucidate the nature of these critical structures.

Johannes Nathanael Lieberkühn (1711-1756): luminary eighteenth century anatomist and his illuminating discovery of intestinal glands

Johannes Nathanael Lieberkühn was a prodigious anatomist whose meticulous experiments and precise detailing helped in comprehending the microscopic anatomy of digestive system during early part of eighteenth century. Notably, his inventions in the field of microscopy aptly complemented his quest for anatomical knowledge at microscopic level. He designed a reflector (Lieberkühn reflector) which enhanced the amount of focussed light leading to bright illumination of tissue specimen. He invented the solar microscope which provided excellent resolution of minute anatomical details. Lieberkühn discovered the digestive juice secreting tubular glands (glands of Lieberkühn) present at the base of intestinal villi producing epithelial invaginations (crypts of Lieberkühn). He also described the intricate juxtaposition of blood vessels in relation to a single intestinal villi. Moreover, through empirically designed experimental set up, Lieberkühn was able to demonstrate the flow of lymph from intestinal villi to collecting lymphatic vessels. Also, his grandiose collection of laboratory specimens involving vascular anatomy are a testimony of his untiring efforts in academia. His contributions were seminal in comprehending the anatomy of digestive system and paved the way for future revelations. His work unveiled the enormous scope of microanatomy in medical science and catalysed the advent of histological staining methods a century later.

Increasing demand for ophthalmic pathology: time trends in a laboratory with nationwide coverage

PURPOSE

To report the time trends in basic patient characteristics and the number of specimens received at a national referral center for ophthalmic pathology.

METHODS

Data on patient sex, age at surgical resection and geographical location of the referring unit were obtained for all specimens received at the St. Erik Ophthalmic Pathology laboratory, Stockholm, Sweden, between January 1^st, 1959, and December 31^st, 2021.

RESULTS

A total of 33 057 specimens had been received, of which 14 560 (44%) came from men and 18 477 (56%) from women (for 20 patients, the sex was not specified). The average annual percent change (AAPC) in the number specimens received was + 10.5%, whereas the Swedish population increased with 0.5% per year. Patients became older throughout the period, with an average yearly increase of patient age at surgery of 0.3 years (AAPC 0.2%). Overall, women were three years older than men at surgery (59.4 versus 56.4 years, P < 0.0001) The number of specimens increased with patient age from the first to the 8^th decade, after which it decreased to zero in the 11^th decade. The largest portion of patients had undergone their surgery in one of the hospitals or clinics in the capital region, with four of the five largest sources corresponding to the most populous counties in the country.

CONCLUSIONS

During six decades, the growth in number of specimens sent to our national referral center for ophthalmic pathology has greatly outpaced the growth of the population, indicating an increasing demand for subspecialized services. Throughout the period, patients have become older, and a higher number of specimens have been submitted from female patients.

Correlative microscopy and block-face imaging (CoMBI): a 3D imaging method with wide applicability in the field of biological science

Correlative microscopy and block-face imaging (CoMBI) is an imaging method, which is characterized by the ability to obtain both serial block-face images as a 3-dimentional (3D) dataset and sections for 2-dimentional (2D) light microscopic analysis. These 3D and 2D morphological data can be correlated with each other to facilitate data interpretation. CoMBI is an easy-to-install and low-cost 3D imaging method since its system can be assembled by the researcher using a regular microtome, consumer digital camera, and some self-made devices, and its installation and instruction manuals are open-source. After the first release of CoMBI method from our laboratory, CoMBI systems have been installed in more than a dozen laboratories and are used for 3D analysis of various biological specimens. Typical application of CoMBI is 3D anatomical analysis using the natural color and contrast of the specimen. We have been using CoMBI for analyzing human brain to obtain the fine 3D anatomy as a reference to determine the causes of neurological diseases and to improve the effectiveness of surgery. Recently, we have been using CoMBI for detecting the colors of chromogens, which are used for labeling specific molecules. Mouse embryos colored with X-gal, a conventional chromogen for detecting LacZ products, were imaged using CoMBI, and the 3D distribution of X-gal was successfully visualized. Thus, CoMBI can now be used for many purposes, including 3D anatomical analysis, 2D microscopy using sections, and 3D distribution of specific molecules. These suggest that CoMBI should be more widely used in the field of biological research.

IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images

Advances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since "seeing is believing", it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital workflows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer.

Is there a Need to Change the Basic Principles of Histology? Educational, Functional and Embryological Perspective

Although it is not an easy task to classify cells into different types, or in turn cell types into tissue types, a clear, understandable, didactically and clinically relevant tissue classification is indispensable for undergraduate medical education, expert discussions in biomedical research as well as for clinical practice. From the earliest discovery of the light microscope on, tissue classification has been a dynamic process. Historically, it was not a rare occurrence that different textbooks offered different tissue classifications. Nowadays, classifications have almost become uniform – the most common is the histological classification into four basic tissue types (epithelial, connective, muscle, nervous), which is recognized by the majority of modern histology and pathology textbooks. The reason is that, with some exceptions, this classification seems to be the most relevant not only for educational purposes but also from an embryological perspective and clinical-histopathological practice. Recently, attempts have been made to abandon this established classification and replace it with a new one. Any new classification, which would improve the presently used is welcomed. However, if the proposed innovation does not satisfy the needs of modern education and clinical practice, it should be handled with great caution or reconsidered.

Use of intercellular proximity labeling to quantify and decipher cell-cell interactions directed by diversified molecular pairs

FucoID is an intercellular proximity labeling technique for studying cell-cell interactions (CCIs) via fucosyltransferase (FT)-meditated fucosyl-biotinylation, which has been applied to probe antigen-specific dendritic cell (DC)-T cell interactions. In this system, bait cells of interest with cell surface-anchored FT are used to capture the interacting prey cells by transferring a biotin-modified substrate to prey cells. Here, we leveraged FucoID to study CCIs directed by different molecular pairs, e.g., programmed cell death protein-1(PD-1)/programmed cell death protein-ligand-1 (PD-L1), and identify unknown or little studied CCIs, e.g., the interaction of DCs and B cells. To expand the application of FucoID to complex systems, we also synthesized site-specific antibody-based FT conjugate, which substantially improves the ability of FucoID to probe molecular signatures of specific CCI when cells of interest (bait cells) cannot be purified, e.g., in clinical samples. Collectively, these studies demonstrate the general applicability of FucoID to study unknown CCIs in complex systems at a molecular resolution.

Is there a Need to Change the Basic Principles of Histology? Educational, Functional and Embryological Perspective

Although it is not an easy task to classify cells into different types, or in turn cell types into tissue types, a clear, understandable, didactically and clinically relevant tissue classification is indispensable for undergraduate medical education, expert discussions in biomedical research as well as for clinical practice. From the earliest discovery of the light microscope on, tissue classification has been a dynamic process. Historically, it was not a rare occurrence that different textbooks offered different tissue classifications. Nowadays, classifications have almost become uniform - the most common is the histological classification into four basic tissue types (epithelial, connective, muscle, nervous), which is recognized by the majority of modern histology and pathology textbooks. The reason is that, with some exceptions, this classification seems to be the most relevant not only for educational purposes but also from an embryological perspective and clinical-histopathological practice. Recently, attempts have been made to abandon this established classification and replace it with a new one. Any new classification, which would improve the presently used is welcomed. However, if the proposed innovation does not satisfy the needs of modern education and clinical practice, it should be handled with great caution or reconsidered.

Multiphoton intravital microscopy of rodents

Tissues are heterogeneous with respect to cellular and non-cellular components and in the dynamic interactions between these elements. To study the behaviour and fate of individual cells in these complex tissues, intravital microscopy (IVM) techniques such as multiphoton microscopy have been developed to visualize intact and live tissues at cellular and subcellular resolution. IVM experiments have revealed unique insights into the dynamic interplay between different cell types and their local environment, and how this drives morphogenesis and homeostasis of tissues, inflammation and immune responses, and the development of various diseases. This Primer introduces researchers to IVM technologies, with a focus on multiphoton microscopy of rodents, and discusses challenges, solutions and practical tips on how to perform IVM. To illustrate the unique potential of IVM, several examples of results are highlighted. Finally, we discuss data reproducibility and how to handle big imaging data sets.

A review on low-cost microscopes for Open Science

This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low-cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes. Moreover, this work includes a discussion on the degree of maturity of the solutions in terms of the adoption of practices aligned with the development of Open Science. RESEARCH HIGHLIGHTS: Concise review on low-cost microscopes for developing Open Science, exposing the role of smartphone-based microscopy. The work classifies microscopes in two main categories: (1) portable field microscopes, and (2) multipurpose automated microscopes.

Automated Open-Hardware Multiwell Imaging Station for Microorganisms Observation

Bright field microscopes are particularly useful tools for biologists for cell and tissue observation, phenotyping, cell counting, and so on. Direct cell observation provides a wealth of information on cells’ nature and physiological condition. Microscopic analyses are, however, time-consuming and usually not easy to parallelize. We describe the fabrication of a stand-alone microscope able to automatically collect samples with 3D printed pumps, and capture images at up to 50× optical magnification with a digital camera at a good throughput (up to 24 different samples can be collected and scanned in less than 10 min). Furthermore, the proposed device can store and analyze pictures using computer vision algorithms running on a low power integrated single board computer. Our device can perform a large set of tasks, with minimal human intervention, that no single commercially available machine can perform. The proposed open-hardware device has a modular design and can be freely reproduced at a very competitive price with the use of widely documented and user-friendly components such as Arduino, Raspberry pi, and 3D printers.

Evolution of Medical Approaches and Prominent Therapies in Breast Cancer

An examination of the origins of medical approaches to breast cancer marks this disease as one of the most difficult to manage. As the early identification, diagnosis and treatment of breast cancer evolve, we will move to a time when each patient and their cancer can be assessed to determine unique patient-specific (personalized) approaches to therapy. Humans have attempted to manage breast cancer for millennia. Even today, the disease claims thousands of lives each year. In light of the increasingly sophisticated understanding of cancer diagnosis and treatment, together with our ultimate failure to offer a cure in the most difficult cases, it is instructive to reflect on the beginnings of our understanding.

Clinical data to be used as a foundation to combat Covid-19 vaccine hesitancy

The coronavirus has become the paramount subject in peoples' lives, affecting and disrupting virtually every aspect of society, as the pandemic casts a shadow over the world. The facts, myths, and conspiracy theories centered on the Covid-19 pandemic have dominated social media accounts, local and national newspapers, as well as television programs. Strategies need to be evolved to counter Covid-19 vaccine hesitancy and mitigate health disparities in at-risk populations. Overcoming misinformation and distrust will require an interdisciplinary approach to deal with Covid-19. The purpose of this review is to offer a factual basis to all healthcare providers to assist in framing strategies to mitigate vaccine hesitancy and achieve herd immunity to combat the deadly Covid-19 pandemic. First an overview of the discovery of the viruses and their molecular structures will be presented. Secondly, a historical perspective is offered, comparing the differences between the 1918 flu pandemic and the current covid-19 pandemic. Lastly, an overview for proposed techniques and methods to counter and or mitigate covid-19 vaccine misinformation that may be used by an interdisciplinary team will be offered narratively and graphically.

Desktop scanning electron microscopy in plant-insect interactions research: a fast and effective way to capture electron micrographs with minimal sample preparation

The ability to visualize cell and tissue morphology at a high magnification using scanning electron microscopy (SEM) has revolutionized plant sciences research. In plant-insect interactions studies, SEM-based imaging has been of immense assistance to understand plant surface morphology including trichomes [plant hairs; physical defense structures against herbivores], spines, waxes, and insect morphological characteristics such as mouth parts, antennae, and legs, that they interact with. While SEM provides finer details of samples, and the imaging process is simpler now with advanced image acquisition and processing, sample preparation methodology has lagged. The need to undergo elaborate sample preparation with cryogenic freezing, multiple alcohol washes, and sputter coating makes SEM imaging expensive, time consuming, and warrants skilled professionals, making it inaccessible to majority of scientists. Here, using a desktop version of SEM (SNE- 4500 Plus Tabletop), we show that the "plug and play" method can efficiently produce SEM images with sufficient details for most morphological studies in plant-insect interactions. We used leaf trichomes of Solanum genus as our primary model, and oviposition by tobacco hornworm (Manduca sexta; Lepidoptera: Sphingidae) and fall armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae), and leaf surface wax imaging as additional examples to show the effectiveness of this instrument and present a detailed methodology to produce the best results with this instrument. While traditional sample preparation can still produce better resolved images with less distortion, we show that even at a higher magnification, the desktop SEM can deliver quality images. Overall, this study provides detailed methodology with a simpler "no sample preparation" technique for scanning fresh biological samples without the use of any additional chemicals and machinery.

A Cell Culture Chip with Transparent, Micropillar-Decorated Bottom for Live Cell Imaging and Screening of Breast Cancer Cells

In the recent years, microfabrication technologies have been widely used in cell biology, tissue engineering, and regenerative medicine studies. Today, the implementation of microfabricated devices in cancer research is frequent and advantageous because it enables the study of cancer cells in controlled microenvironments provided by the microchips. Breast cancer is one of the most common cancers in women, and the way breast cancer cells interact with their physical microenvironment is still under investigation. In this study, we developed a transparent cell culture chip (Ch-Pattern) with a micropillar-decorated bottom that makes live imaging and monitoring of the metabolic, proliferative, apoptotic, and morphological behavior of breast cancer cells possible. The reason for the use of micropatterned surfaces is because cancer cells deform and lose their shape and acto-myosin integrity on micropatterned substrates, and this allows the quantification of the changes in morphology and through that identification of the cancerous cells. In the last decade, cancer cells were studied on micropatterned substrates of varying sizes and with a variety of biomaterials. These studies were conducted using conventional cell culture plates carrying patterned films. In the present study, cell culture protocols were conducted in the clear-bottom micropatterned chip. This approach adds significantly to the current knowledge and applications by enabling low-volume and high-throughput processing of the cell behavior, especially the cell–micropattern interactions. In this study, two different breast cancer cell lines, MDA-MB-231 and MCF-7, were used. MDA-MB-231 cells are invasive and metastatic, while MCF-7 cells are not metastatic. The nuclei of these two cell types deformed to distinctly different levels on the micropatterns, had different metabolic and proliferation rates, and their cell cycles were affected. The Ch-Pattern chips developed in this study proved to have significant advantages when used in the biological analysis of live cells and highly beneficial in the study of screening breast cancer cell–substrate interactions in vitro.

Single-Molecule Narrow-Field Microscopy of Protein-DNA Binding Dynamics in Glucose Signal Transduction of Live Yeast Cells

Single-molecule narrow-field microscopy is a versatile tool to investigate a diverse range of protein dynamics in live cells and has been extensively used in bacteria. Here, we describe how these methods can be extended to larger eukaryotic, yeast cells, which contain subcellular compartments. We describe how to obtain single-molecule microscopy data but also how to analyze these data to track and obtain the stoichiometry of molecular complexes diffusing in the cell. We chose glucose-mediated signal transduction of live yeast cells as the system to demonstrate these single-molecule techniques as transcriptional regulation is fundamentally a single-molecule problem-a single repressor protein binding a single binding site in the genome can dramatically alter behavior at the whole cell and population levels.

A Next Generation of Advances in Chromosome Architecture

New insight into the architecture of chromosomes, their molecular composition, structure and spatial location, and time-resolved features, has grown enormously through developments of a range of pioneering interdisciplinary approaches that lie at the interface of the life and physical sciences. These involve several state-of-the-art "physics of life" tools that are both experimental and theoretical, used in conjunction with molecular biology methods which enable investigation of chromosome structure and function in vitro, in vivo, and even in silico. In particular, a move towards far greater quantitation has enabled transformative leaps in our understanding. These have involved valuable improvements to the spatial and temporal resolution of quantitative measurements, such as in vivo super-resolved light microscopy and single-molecule biophysics methods, which facilitate probing of dynamic chromosome processes hitherto impossible. Similarly, there have been important advances in the theoretical biophysics approaches which have enabled advances in predictive modeling to generate new understanding of the modes of operation of chromosomes across all domains of life. Here, I discuss these advances, and review the current state of our knowledge of chromosome architecture and speculation where future advances may lead.

An alternative approach to tracing the volumic proliferation development of an entire tumor spheroid in 3D through a mini-Opto tomography platform

Microscopy, which is listed among the major in-situ imaging applications, allows to derive information from a biological sample on the existing architectural structures of cells and tissues and their changes over time. Large biological samples such as tumor spheroids cannot be imaged within one field of view, regional imaging in different areas and subsequent stitching are required to attain the full picture. Microscopy is not typically used to produce full-size visualization of tumor spheroids measuring a few millimeters in size. In this study, we propose a 3D volume imaging technique for tracing the growth of an entire tumor spheroid measuring up to 10 mm using a miniaturized optical (mini-Opto) tomography platform. We performed a primary analysis of the 3D imaging for the MIA PaCa-2 pancreatic tumoroid employing its 2D images produced with the mini-Opto tomography from different angles ranging from -25 ° to +25 ° at six different three-day-apart time points of consecutive image acquisition. These 2D images were reconstructed by using a 3D image reconstruction algorithm that we developed based on the algebraic reconstruction technique (ART). We were able to reconstruct the 3D images of the tumoroid to achieve 800 × 800-pixel 50-layer images at resolutions of 5-25 μm. We also created its 3D visuals to understand more clearly how its volume changed and how it looked over weeks. The volume of the tumor was calculated to be 6.761 mm³ at the first imaging time point and 46.899 mm³ 15 days after the first (at the sixth time point), which is 6.94 times larger in volume. The mini-Opto tomography can be considered more advantageous than commercial microscopy because it is portable, more cost-effective, and easier to use, and enables full-size visualization of biological samples measuring a few millimeters in size.

MicroHikari3D: an automated DIY digital microscopy platform with deep learning capabilities

A microscope is an essential tool in biosciences and production quality laboratories for unveiling the secrets of microworlds. This paper describes the development of MicroHikari3D, an affordable DIY optical microscopy platform with automated sample positioning, autofocus and several illumination modalities to provide a high-quality flexible microscopy tool for labs with a short budget. This proposed optical microscope design aims to achieve high customization capabilities to allow whole 2D slide imaging and observation of 3D live specimens. The MicroHikari3D motion control system is based on the entry level 3D printer kit Tronxy X1 controlled from a server running in a Raspberry Pi 4. The server provides services to a client mobile app for video/image acquisition, processing, and a high level classification task by applying deep learning models.

Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology

Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Construction of a novel asymmetric imidazole-cored AIE probe for ratiometric imaging of endogenous leucine aminopeptidase

We report a rational strategy to deliberately construct the first asymmetric tetraarylimidazole-based AIE probe, integrating AIE behavior in synergy with ESIPT character to image endogenous LAP for the first time. It offered good sensitivity and selectivity, and concomitantly, was applied successfully for real-time tracking of LAP in the cisplatin-induced liver injury zebrafish model.

Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes

Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.

Nanoscape, a data-driven 3D real-time interactive virtual cell environment

Our understanding of cellular and structural biology has reached unprecedented levels of detail, and computer visualisation techniques can be used to create three-dimensional (3D) representations of cells and their environment that are useful in both teaching and research. However, extracting and integrating the relevant scientific data, and then presenting them in an effective way, can pose substantial computational and aesthetic challenges. Here we report how computer artists, experts in computer graphics and cell biologists have collaborated to produce a tool called Nanoscape that allows users to explore and interact with 3D representations of cells and their environment that are both scientifically accurate and visually appealing. We believe that using Nanoscape as an immersive learning application will lead to an improved understanding of the complexities of cellular scales, densities and interactions compared with traditional learning modalities.

Correlative microscopy and block-face imaging (CoMBI) method for both paraffin-embedded and frozen specimens

Correlative microscopy and block-face imaging (CoMBI), a method that we previously developed, is characterized by the ability to correlate between serial block-face images as 3-dimensional (3D) datasets and sections as 2-dimensional (2D) microscopic images. CoMBI has been performed for the morphological analyses of various biological specimens, and its use is expanding. However, the conventional CoMBI system utilizes a cryostat, which limits its compatibility to only frozen blocks and the resolution of the block-face image. We developed a new CoMBI system that can be applied to not only frozen blocks but also paraffin blocks, and it has an improved magnification for block-face imaging. The new system, called CoMBI-S, comprises sliding-type sectioning devices and imaging devices, and it conducts block slicing and block-face imaging automatically. Sections can also be collected and processed for microscopy as required. We also developed sample preparation methods for improving the qualities of the block-face images and 3D rendered volumes. We successfully obtained correlative 3D datasets and 2D microscopic images of zebrafish, mice, and fruit flies, which were paraffin-embedded or frozen. In addition, the 3D datasets at the highest magnification could depict a single neuron and bile canaliculus.

Quantitative skills in undergraduate neuroscience education in the age of big data

For over a half-Century, the mathematics requirement for graduation at most undergraduate colleges and universities has been one year of calculus and a semester of statistics. Many universities and colleges offer a neuroscience major that may or may not add additional mathematics, statistics, or data science requirements. Today in the age of Big Data and Systems Neuroscience, many students are ill-equipped for the future without the tools of computational competency that are necessary to tackle the large data sets generated by contemporary neuroscience research. Required courses in statistics still focus on parametric statistics based on the normal distribution and do not provide the computational tools required to analyze big data sets. Undergraduates in STEM fields including neuroscience need to enroll in the Data Science courses that are required in the social sciences (e.g., economics, political science and psychology). Contemporary systems neuroscience is routinely done by interdisciplinary research teams of statisticians, engineers, and physical scientists. Emerging "NeuroX-omics" such as connectomics have emerged along with genomics, proteomics, and transcriptomics, all of which deploy systems analysis techniques based on mathematical graph theory. Connectomics is the 21st Century's functional neuroanatomy. Whole brain connectome research appears almost monthly in the Drosphila, zebra fish, and mouse literature, and human brain connectomics is not far behind. The techniques for connectomics rely on the tools of data science. Undergraduate neuroscience students are already squeezed for credit hours given the high-prescribed science curriculum for biology majors and premedical students, in addition to required courses in social sciences and humanities. However, additional training in mathematics, statistics, computer science, and/or data science is urgently needed for undergraduate neuroscience majors just to understand the contemporary research literature. Undoubtedly, the faculty who teach neuroscience courses are acutely aware of the problem and most of them freely acknowledge the importance of quantitative analytical skills for their students. However, some faculty members may feel that their own math and statistics knowledge or other analytical skills have atrophied beyond recall or were never fulfilled in the first place. In this commentary I suggest that this problem can be ameliorated, though not solved, through organizing workshops, journal clubs, or independent studies courses in which the students and the instructors learn and teach each other in short-course format. In addition, web-available teaching materials such as targeted video clips are plentifully available on the internet. To attract and maintain student interest, qauntitative instruction and learning should occur in neuroscience context.

Strategies for monitoring cell-cell interactions

Multicellular organisms depend on physical cell-cell interactions to control physiological processes such as tissue formation, neurotransmission and immune response. These intercellular binding events can be both highly dynamic in their duration and complex in their composition, involving the participation of many different surface and intracellular biomolecules. Untangling the intricacy of these interactions and the signaling pathways they modulate has greatly improved insight into the biological processes that ensue upon cell-cell engagement and has led to the development of protein- and cell-based therapeutics. The importance of monitoring physical cell-cell interactions has inspired the development of several emerging approaches that effectively interrogate cell-cell interfaces with molecular-level detail. Specifically, the merging of chemistry- and biology-based technologies to deconstruct the complexity of cell-cell interactions has provided new avenues for understanding cell-cell interaction biology and opened opportunities for therapeutic development.

In Vivo and In Situ Approach to Study Islet Microcirculation: A Mini-Review

The pancreas is regarded as consisting of two separate organ systems, the endocrine and exocrine pancreas. While treatment of a disease with either an endocrine or exocrine pathogenesis may affect the function of the entire pancreas, the pancreatic diseases have been treated by clinicians in different medical disciplines, including endocrinologists and gastroenterologists. Islet microcirculation has long been considered to be regulated independently from that of the exocrine pancreas. A new model proposes that pancreatic islet blood flow is integrated with the surrounding exocrine capillary network. This recent model may provide revived or contrasting hypotheses to test, since the pancreatic microcirculation has critical implications for the regulation of islet hormones as well as acinar pancreas functions. In this mini-review, practical applications of in vivo and in situ studies of islet microcirculation are described with a specific emphasis on large-scale data analysis to ensure sufficient sample size accounting for known islet heterogeneity. For in vivo small animal studies, intravital microscopy based on two-photon excitation microscopes is a powerful tool that enables capturing the flow direction and speed of individual fluorescent-labeled red blood cells. Complementarily, for structural analysis of blood vessels, the recent technical advancements of confocal microscopy and tissue clearing have enabled us to image the three-dimensional network structure in thick tissue slices.

A new approach to analysis of intracellular proteins and subcellular localization using cellprofiler and imageJ in combination

Analytical pipeline, which is used for various analysis application, of CellProfiler, an open-source software for cell imaging analysis, is very important. In the present study, to examine whether intracellular proteins can be discriminated using a combination of CellProfiler and ImageJ, we analyzed neuroblastoma and monocytic cell lines, and disease-specific induced pluripotent stem cell (iPSC)-derived neurons. This revealed that scattered puncta of Rab7 and transferrin in neuroblastoma lines were clearly detectable by created analytical pipelines in CellProfiler. We then constructed pipelines for measuring the distance from the center of the nucleus to allow investigation of the intracellular localization of Rab7 or transferrin. Using CellProfiler and ImageJ in combination, we confirmed that our pipelines were applicable both quantitatively and objectively to analysis of membrane trafficking of proteins such as Rab proteins and transferrin. In addition, when applied to quantitative measurement of phagocytosis, our pipelines clearly detected monocytic cell lines that had engulfed bioparticles. Finally, we developed new pipelines for analysis of disease phenotype using iPSCs from a patient with familial Parkinson's disease (PD), harboring the I2020T LRRK2 mutation (PARK8). These were able to successfully detect Rab5 puncta and Rab7 puncta in PARK8 patient iPSC-derived neurons. Interestingly, in long-term culture, we found that the numbers of Rab7 puncta in a single PARK8 patient iPSC-derived neurons were lower than that of control iPSC-derived neurons. On the other hands, at 14 days in vitro, the numbers of Rab5 puncta in PARK8 patient iPSC-derived neurons were lower than those of isogenic iPSC-derived neurons, but not Rab7 puncta. Furthermore, Rab5 puncta of PARK8 patient iPSC-derived neurons exhibited distinct localization pattern relative to isogenic iPSC-derived neurons. These present results suggest that this new analytical tool can be used as a supporting method for quantification of intracellular protein.

Cypsela diversity in some members of Compositae through LM study and its taxonomic significance

Compositae (Asteraceae), also known as the sunflower family has evolved to become the most diverse and advanced angiosperm family. However, with high diversity, taxonomic complexities also arise at several levels. A reliable tool in resolving such taxonomic conundrums in this family is the characteristic fruit of Compositae known as "cypsela." While most of the previous cypsela-based studies have focused on specific tribes and species of Compositae, in this study, we shift our focus to the genus level and seek a broader understanding of the taxonomic relationships that prevail in this family. In order to achieve this, we sampled 25 genera of Compositae and subjected them to qualitative and quantitative analysis to resolve them into groups based on the degree of similarity. This study was conducted by employing light microscopy techniques for gathering the qualitative and quantitative morphological data of the cypselae. The qualitative data were collected on six key morphological characteristics-shape, color, base, surface ornamentation, ribs, and pappus types for all the members. These data were used to yield an artificial dichotomous key to genera for the 25 members. The quantitative data on dimensions (length, breadth) of the entire cypsela as well as the pappus and ribs were subjected to principal component analysis, to understand the covariance among these variables. Hierarchical clustering followed by dendrogram construction was used to visualize the patterns of correlation within the samples and make taxonomic conclusions. The resulting dendrogram showed four closely related clades that consisted of 23 out of the 25 members whereas 2 members emerged as outgroups. The results of this study commensurate with DNA-based resolution of the concerned Compositae members, hence highlighting the reliability and significance of both light microscopy and morphology-based studies that seem to be fading away otherwise.

A new interpretation of the human embryo drawings in Icones Embryonum Humanorum by Samuel Thomas Soemmerring

In 1799, Samuel Thomas Soemmerring published the book Icones Embryonum Humanorum, which was one of the first attempts in history to sort out prenatal human development chronologically. Despite its importance for the anatomical sciences, there is little information about Icones. In this context, our objective was to identify and estimate the developmental age of the seven human embryos present in Icones Embryonum Humanorum by external morphological analysis and morphometry of the drawings using Image-J^® software. First, the book was translated from Latin. Then, the developmental age was estimated by external morphological analysis and morphometry (greatest length) of the drawings using Image-J^® software. The book is composed of 20 drawings of human embryos and fetuses from two life-size tables. According to the external features and morphometric analysis, there are seven embryos (drawings I-VII). The embryonic age (pf: post-fertilization age) of drawing I corresponds to day 29-31 pf; drawing II, to day 33-35 pf; drawing III, to day 37-40 pf; drawing IV, to day 42-45 pf; drawing V, to day 45-47 pf; drawing VI, today 47-50 pf; and drawing VII, to day 52-55 pf. There are differences between the development age estimated by Soemmerring and our analysis. These differences are probably due to the methodological and technical limitations of the eighteenth century.

The construction of high-magnification homemade lenses for a simple microscope: an easy "DIY" tool for biological and interdisciplinary education

The rise of microscopy in the seventeenth century allowed scientists to discover a new world of microorganisms and achieve great physiological advances. One of the first microscopes of the epoch was Antonie van Leeuwenhoek's microscope, a deceptively simple device that contains a single ball lens housed in a metal plate allowing the observation of samples at up to ×250 magnification. Such magnification was much greater than that achieved by rudimentary compound microscopes of the era, allowing for the discovery of microscopic, single-celled life, an achievement that marked the study of biology up to the nineteenth century. Since Leeuwenhoek's design uses a single ball lens, it is possible to fabricate variations for educational activities in physics and biology university and high school classrooms. A fundamental problem, however, with home-built microscopes is that it is difficult to work with glass. We developed a simple protocol to make ball lenses of glass and gelatin with high magnification that can be done in a university/high school classroom, and we designed an optimized support for focusing and taking photographs with a smartphone. The protocol details a simple, easily accessible, low-cost, and effective tool for the observation of microscopic samples, possible to perform anywhere without the need for a laboratory or complex tools. Our protocol has been implemented in classrooms in Chile to a favorable reception.

Graduate Student Literature Review: Understanding the genetic mechanisms underlying mastitis

Mastitis is the costliest disease facing dairy producers today; consequently, it has been the subject of substantial research focus. Efforts have evolved from an initial focus on understanding the etiology of intramammary infections to the application of preventative measures, including attempts to breed cows that are resistant to infection. However, breeding for resistance to infection has proven difficult, given the complexity of the disease and the high expense associated with assembling high-quality genotypes and phenotypes. This review provides a brief background on mastitis; illustrates current understanding of the genetics influencing mastitis and the application of this knowledge; and discusses challenges and limitations in understanding these mechanisms and applying these findings to genetic improvement strategies.

Enzyme-targeted fluorescent small-molecule probes for bacterial imaging

Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.

Robotic microscopy for everyone: the OpenFlexure microscope

Optical microscopes are an essential tool for both the detection of disease in clinics, and for scientific analysis. However, in much of the world access to high-performance microscopy is limited by both the upfront cost and maintenance cost of the equipment. Here we present an open-source, 3D-printed, and fully-automated laboratory microscope, with motorised sample positioning and focus control. The microscope is highly customisable, with a number of options readily available including trans- and epi- illumination, polarisation contrast imaging, and epi-florescence imaging. The OpenFlexure microscope has been designed to enable low-volume manufacturing and maintenance by local personnel, vastly increasing accessibility. We have produced over 100 microscopes in Tanzania and Kenya for educational, scientific, and clinical applications, demonstrating that local manufacturing can be a viable alternative to international supply chains that can often be costly, slow, and unreliable.