Biological Materials Research Articles

The wildcat (Felis s. silvestris) in the Mediterranean forest: sighting through photo-trapping and non-invasive hair collection for genetic purposes.

The European wildcat (Felis silvestris silvestris) is a mesocarnivore species widely distributed in Europe, from Eastern Europe to Portugal and from Scotland to Italy. Recent biogeographical studies of wildcat populations have endeavoured to assess in detail the various issues that pose a threat to this species, including hybridization with domestic cats. The use of non-invasive sampling methods supported by photo-trapping and some attractants has made it possible to gather genetic material for the detection of native wildcats in locally threatened populations, some of which live in the Iberian Peninsula. Testimonies of naturalists, hunters and farm workers led our team to choose specific areas in two large territories of Mediterranean forests where the presence of wildcats has been historically attested: the Almonte River basin and the Sierra de San Pedro Mountains. Between 2014 and 2018, non-invasive hair sampling was performed using valerian (Valeriana officinalis) as an attractant and supported by photo-trapping to guarantee the collection of genuine biological material (hair samples). The hair samples were genetically assessed by sequencing the nuclear gene IRBP (interphotoreceptor retinoid-binding protein) and the mtDNA gene ND4 (NADH dehydrogenase subunit 4). Despite the low density of wildcats, this combined protocol proved to be an applicable tool for detecting the presence of elusive wildcats and other mesocarnivore species in this remote region of southern Europe. In addition, non-invasive hair trapping contributes to the collection of genetic material from current wildcat populations. This procedure could enhance future management actions focused on collecting quality individualized biological material.

A device for rapid calorimetric measurements on small biological tissue samples

AbstractA new calorimetric technique is described that allows high-throughput heat production rate measurements on small biological tissue samples. The technique is based on the widely used thermopile chip technology combined with an innovative method for precise transport and positioning of samples of different biological materials at the thermal power detector inside the calorimeter. The new transport and positioning technique is a combination of fluidic and mechanical transport, where the latter is realized by a magneto-motor drive. The transport facility ensures good diffusive oxygen penetration into the sample, which is essential for highly metabolically active materials. The proper functioning of the device is demonstrated by measuring the heat production of metabolically active brown adipose tissue, biopsied tegu lizard muscle, and live Drosophila larvae at different stages and temperatures.

Genetic tests as the strongest motivator of cooperation between participants and biobanks–Findings from cross-sectional study

IntroductionThe development of the scientific potential linked with biobanking and research on human biological material is highly dependent on the willingness of potential donors to cooperate with entities that collect the material. For this reason, it is crucial to identify the circumstances and factors that may encourage potential participants to donate their biological material. In particular, knowledge of the motivational factors that can be modified by the persons managing a biobank may prove notably important for shaping the organizational and communication policy of the biobank and other scientific institutions.Material and methodsThe research was carried out on a group of 1,100 people over 18 years of age representing the adult population of Poland in 2021.ResultsMore than half of the respondents declared their willingness to donate a blood sample for research purposes to a biobank (57.8%). The most often indicated incentives among the factors supporting the donation of biological material were offers of: obtaining the results of genetic tests predicting the risk of diseases (77.1%), blood tests (71.3%), the possibility of obtaining a small remuneration (64.6%) and the carrying out of genetic ancestry tests (60.4%).ConclusionOffering the possibility of performing additional diagnostic tests, especially genetic tests, may significantly increase the willingness of potential donors to cooperate with biobanks and other entities collecting human biological material for the purpose of scientific research. However, attention should also be paid to the challenges and risks linked with respecting the privacy and autonomy of research participants.

Spatial and Temporal Resolution of Cyanobacterial Bloom Chemistry Reveals an Open-Ocean Trichodesmium thiebautii as a Talented Producer of Specialized Metabolites.

While the ecological role that Trichodesmium sp. play in nitrogen fixation has been widely studied, little information is available on potential specialized metabolites that are associated with blooms and standing stock Trichodesmium colonies. While a collection of biological material from a T. thiebautii bloom event from North Padre Island, Texas, in 2014 indicated that this species was a prolific producer of chlorinated specialized metabolites, additional spatial and temporal resolution was needed. We have completed these metabolite comparison studies, detailed in the current report, utilizing LC-MS/MS-based molecular networking to visualize and annotate the specialized metabolite composition of these Trichodesmium blooms and colonies in the Gulf of Mexico (GoM) and other waters. Our results showed that T. thiebautii blooms and colonies found in the GoM have a remarkably consistent specialized metabolome. Additionally, we isolated and characterized one new macrocyclic compound from T. thiebautii, trichothilone A (1), which was also detected in three independent cultures of T. erythraeum. Genome mining identified genes predicted to synthesize certain functional groups in the T. thiebautii metabolites. These results provoke intriguing questions of how these specialized metabolites affect Trichodesmium ecophysiology, symbioses with marine invertebrates, and niche development in the global oligotrophic ocean.

Numerical modeling of inkjet cell output under the interplay of cell-laden bioink consumption and sedimentation

Inkjet printing utilizes the bioink involving biological materials and living cells to generate cell-laden droplets for precise construction of 3D tissue/organ models in a layer-by-layer manner. While printing, the suspended cells in bioink sediment due to predominant gravitational force, and form cell aggregates. It is increasingly difficult to transfer aggregates to the nozzle dispenser, resulting in gradual decay of the cell output, which becomes a critical challenge significantly affecting printing reliability and quality. This study has proposed a computational model coupling the cell flow field due to cell sedimentation and the bioink flow field due to bioink consumption. The modeled cell output has been validated by the experimental results showing a good agreement. Precise prediction of cell output enables optimization of the bioprinting process with less trial-and-error cost and promotes fabrication of more consistent and reproducible bioconstructs. The study finds that (1) the measured cell sedimentation velocity at bioink reservoir bottom increases due to the greater cell aggregates formed while printing; (2) the cell movement dynamics revealed by the model exhibit reduced movement from the sides towards the center of the bioink reservoir due to an increased sedimentation effect over printing; (3) the cell output decreases by 75 % within 60-minute printing at 400 Hz frequency. Applying greater inkjet frequency from 200 to 1000 Hz enables greater cell output efficiency from 0.48 to 0.93; (4) under 75 % preset efficiency criterion, applying frequency > 97 Hz for 60-minute printing is recommended to secure positive cell output considering the minimal threshold to counter sedimentation.

Novel biomarker profiles to improve individual diagnosis and prognosis in patients with suspected inflammatory bowel disease: protocol for the Nordic inception cohort study (NORDTREAT)

IntroductionInflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease, can be challenging to diagnose, and treatment outcomes are difficult to predict. In the NORDTREAT cohort study, a Nordic prospective...

The Politics of Expertise in Genomics Policy and Law

Genomics and biotechnology have generated controversy for decades, about the moral limits of tinkering with and commodifying life, the boundary between nature and technology, the respectful treatment of research participants, and the proper evaluation of emerging technologies. Socio-legal and science and technology studies scholars have demonstrated how the resolution of these questions has serious implications for both science and the law, including the appropriate conduct and direction of scientific research and the construction of legal categories and rights. This article demonstrates that these conflicts also have profound impacts on the politics of science and technology, and particularly approaches to relevant knowledge and expertise. Humanities, social scientific, legal, and lay knowledge asserted themselves through the establishment of human genetics research and battles over the ownership of biological materials and data. However, US political culture—which favors technical and market knowledge—constrained their authority. Cross-national comparison highlights this finding, as other jurisdictions have been more inclusive in their approaches to science and technology governance.

Seven genome sequences of airborne, bacterial isolates from Antarctica.

Ice-covered and remote landscapes in the McMurdo Dry Valleys, Antarctica, are likely seeded by aeolian transport of biological material from ice-free local or distant environments. Here, we report the genome sequences of seven bacteria isolated from aerosols collected on top of two dry valley glaciers.

Using eDNA to play whack-a-mole with invasive species in green yard waste.

As large cities begin to overrun their landfill capacities, they begin to look for alternative locations to handle the waste stream. Seeing an opportunity to bring in revenue, rural communities offer to handle municipal waste in their landfills. However, many rural communities are also places of agricultural production, which are vulnerable to attacks by invasive insect species, which could be present in green yard waste, the component of municipal waste most likely to contain agriculturally harmful insect species. We used environmental DNA (eDNA) to determine whether green yard waste could be a pathway for invasive insect species to enter and establish in the landfill-receiving agricultural community. We identified several target species that could be in green yard waste coming from Vancouver, BC, Canada, to Central Washington State, USA. We sampled green yard waste from 3 sites every 2 weeks from June to October in 2019 and 2020. DNA was extracted from the nearly 400 samples and subjected to amplification with COI barcoding primers followed by sequencing to identify target insects in the samples. Sequence analyses identified 3 species from the target list: 2 species that are pests of deciduous tree fruits and a generalist root-feeding crop pest. This eDNA technique was useful in identifying potential invasive species in green yard waste and may prove to be an important tool informing policy on the movement of biological material across borders and stemming the spread of invasive species.

Ultrastructural 3D Microscopy for Biomedicine: Principles, Applications, and Perspectives.

Modern biomedical research often requires a three-dimensional microscopic analysis of the ultrastructure of biological objects and materials. Conceptual technical and methodological solutions for three-dimensional structure reconstruction are needed to improve the conventional optical, electron, and probe microscopy methods, which to begin with allow one to obtain two-dimensional images and data. This review discusses the principles and potential applications of such techniques as serial section transmission electron microscopy; techniques based on scanning electron microscopy (SEM) (array tomography, focused ion beam SEM, and serial block-face SEM). 3D analysis techniques based on modern super-resolution optical microscopy methods are described (stochastic optical reconstruction microscopy and stimulated emission depletion microscopy), as well as ultrastructural 3D microscopy methods based on scanning probe microscopy and the feasibility of combining them with optical techniques. A comparative analysis of the advantages and shortcomings of the discussed approaches is performed.

Development of small molecule drugs targeting immune checkpoints.

Immune checkpoint inhibitors (ICIs) are used to relieve and refuel anti-tumor immunity by blocking the interaction, transcription, and translation of co-inhibitory immune checkpoints or degrading co-inhibitory immune checkpoints. Thousands of small molecule drugs or biological materials, especially antibody-based ICIs, are actively being studied and antibodies are currently widely used. Limitations, such as anti-tumor efficacy, poor membrane permeability, and unneglected tolerance issues of antibody-based ICIs, remain evident but are thought to be overcome by small molecule drugs. Recent structural studies have broadened the scope of candidate immune checkpoint molecules, as well as innovative chemical inhibitors. By way of comparison, small molecule drug-based ICIs represent superior oral bioavailability and favorable pharmacokinetic features. Several ongoing clinical trials are exploring the synergetic effect of ICIs and other therapeutic strategies based on multiple ICI functions, including immune regulation, anti-angiogenesis, and cell cycle regulation. In this review we summarized the current progression of small molecule ICIs and the mechanism underlying immune checkpoint proteins, which will lay the foundation for further exploration.

Ultrasensitive and Highly Selective Detection of Staphylococcus aureus at the Single-Cell Level Using Bacteria-Imprinted Polymer and Vancomycin-Conjugated MnO2 Nanozyme.

Pathogenic bacterial infections, even at extremely low concentrations, pose significant threats to human health. However, the challenge persists in achieving high-sensitivity bacterial detection, particularly in complex samples. Herein, we present a novel sandwich-type electrochemical sensor utilizing bacteria-imprinted polymer (BIP) coupled with vancomycin-conjugated MnO2 nanozyme (Van@BSA-MnO2) for the ultrasensitive detection of pathogenic bacteria, exemplified by Staphylococcus aureus (S. aureus). The BIP, in situ prepared on the electrode surface, acts as a highly specific capture probe by replicating the surface features of S. aureus. Vancomycin (Van), known for its affinity to bacterial cell walls, is conjugated with a Bovine serum albumin (BSA)-templated MnO2 nanozyme through EDC/NHS chemistry. The resulting Van@BSA-MnO2 complex, serving as a detection probe, provides an efficient catalytic platform for signal amplification. Upon binding with the captured S. aureus, the Van@BSA-MnO2 complex catalyzes a substrate reaction, generating a current signal proportional to the target bacterial concentration. The sensor displays remarkable sensitivity, capable of detecting a single bacterial cell in a phosphate buffer solution. Even in complex milk matrices, it maintains outstanding performance, identifying S. aureus at concentrations as low as 10 CFU mL-1 without requiring intricate sample pretreatment. Moreover, the sensor demonstrates excellent selectivity, particularly in distinguishing target S. aureus from interfering bacteria of the same genus at concentrations 100-fold higher. This innovative method, employing entirely synthetic materials, provides a versatile and low-cost detection platform for Gram-positive bacteria. In comparison to existing nanozyme-based bacterial sensors with biological recognition materials, our assay offers distinct advantages, including enhanced sensitivity, ease of preparation, and cost-effectiveness, thereby holding significant promise for applications in food safety and environmental monitoring.

Environmental Factors Affecting the Concentration of DNA in Blood and Saliva Stains: A Review

DNA evidence has now become an essential part of forensic investigations since it offers vital information for person identification and crime resolution. However, the biological material is affected by some environmental factors which may impact the DNA in biological samples. This may affect the correctness and reliability of forensic DNA analysis. This review is related to the influence of various environmental conditions on the stability and degradation of DNA in biological stains including blood and saliva stains. The common factors that affect DNA are temperature, humidity, exposure to sunlight, and type of substrate. The information is crucial to improve forensic DNA analysis and forensic protocol optimization. The DNA stability and integrity in biological materials, such as blood and saliva stains, are indispensable for forensic DNA analysis. Environmental influences, however, significantly affect DNA concentration and may jeopardize forensic analysis. The present review explores various environmental factors for their effect on DNA stability in blood and saliva stains. While DNA degradation is slowed but not completely prevented by low temperatures, it is accelerated by high temperatures. Risks of contamination arise from the promotion of microbial growth and DNA breakdown by humidity. DNA photodamage brought on by sunlight exposure results in strand breakage and cross-linking. DNA stability is also influenced by the type of substrate used; porous surfaces, such as cloth, are better at keeping fluids than non-porous ones, such as glass. Maintaining the integrity of DNA evidence requires an understanding of these variables. The present studies will help to create sophisticated DNA preservation methods for use in forensic DNA examination. The study emphasizes the requirement of improvement in forensic DNA analysis skills, related to the preservation of DNA pieces of evidence and the possible effect of environmental factors.

Comparison of the Effect of Platelet-rich Plasma (PRP) and Fat Graft on Autologous Bone Grafting in a Randomized-controlled Experimental Skull Model.

Gold standard method for the treatment of critical-sized bone defects is the autogenous bone grafting procedure. A number of new and potentially useful adjuncts currently are being investigated to enhance the success of bone grafting. We propose to evaluate the effect of the most known and easily obtained 2 biological materials, fat graft and platelet-rich plasma (PRP), on bone graft healing. Twenty-seven New Zealand male rabbits were included in this randomized, controlled study. Two-sided 15-mm diameter bone defects were created in the parietal bones and the bones taken were replaced right-to-left and vice versa with 1 control group, 1 fat graft applied group, and the last one PRP applied group. Histologic evaluation and 3-dimensional maxillofacial computerized tomography were performed and bone density was calculated. In radiologic analysis, bone density was significantly different in the PRP group compared with the control and fat graft group in the 12th week (P<0.05). In histologic scoring analysis, the PRP group had a better score than the control and fat graft group, while the fat graft group was worse than the control group in the 6th week (P<0.05). The addition of PRP had a positive effect whereas fat graft had a negative effect on bone graft healing compared with the control group.

REPROGRAMMING FILAMENTOUS FD VIRUSES TO CAPTURE COPPER IONS.

C-terminal truncated variants (A, VA, NVA, ANVA, FANVA and GFANVA) of our recently identified Cu(II) specific peptide "HGFANVA" were displayed on filamentous fd phages. Wild type fd-tet and engineered virus variants were treated with 100 mM Cu(II) solution at a final phage concentration of 1011vir/ml and 1012vir/ml. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) imaging before Cu(II) exposure showed»6-8 nm thick filamentous virus layer formation. Cu(II) treatment resulted in aggregated bundle-like assemblies with mineral deposition. HGFANVA phage formed aggregates with an excessive mineral coverage. As the virus concentration was 10-fold decreased, nanowire-like assemblies were observed for shorter peptide variants A, NVA and ANVA. Wild type fd phages did not show any mineral formation. Energy dispersive X-ray spectroscopy (EDX) analyses revealed the presence of C and N peaks on phage organic material. Cu peak was only detected for engineered viruses. Metal ion binding of viruses was next investigated by enzyme-linked immunosorbent assay (ELISA) analyses. Engineered viruses were able to bind Cu(II) forming mineralized intertwined structures although no His (H) unit was displayed. Such genetically reprogrammed virus based biological materials can be further applied for bioremediation studies to achieve a circular economy.

Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment.

Cable bacteria, characterized by their multicellular filamentous growth, are prevalent in both freshwater and marine sediments. They possess the unique ability to transport electrons over distances of centimeters. Coupled with their capacity to fix CO2 and their record-breaking conductivity for biological materials, these bacteria present promising prospects for bioprocess engineering, including potential electrochemical applications. However, the cultivation of cable bacteria has been limited to their natural sediment, constraining their utility in production processes. To address this, our study designs synthetic sediment, drawing on ion exchange chromatography data from natural sediments and existing literature on the requirements of cable bacteria. We examined the effects of varying bentonite concentrations on water retention and the impacts of different sands. For the first time, we cultivated cable bacteria on synthetic sediment, specifically the freshwater strain Electronema aureum GS. This cultivation was conducted over 10 weeks in a specially developed sediment bioreactor, resulting in an increased density of cable bacteria in the sediment and growth up to a depth of 5 cm. The creation of this synthetic sediment paves the way for the reproducible cultivation of cable bacteria. It also opens up possibilities for future process scale-up using readily available components. This advancement holds significant implications for the broader field of bioprocess engineering.

Transcriptomics and metabolomics: Challenges of studying obesity in osteoarthritis

ObjectiveObesity is a leading risk factor for both the incidence and progression of osteoarthritis (OA). Omic technologies, including transcriptomics and metabolomics are capable of identifying RNA and metabolite profiles in tissues and biofluids of OA patients. The objective of this review is to highlight studies using transcriptomics and metabolomics that contribute to our understanding of OA pathology in relation to obesity. DesignWe conducted a targeted search of PUBMED for articles, and GEO for datasets, published up to February 13, 2024, screening for those using high-throughput transcriptomic and metabolomic techniques to study human or pre-clinical animal model tissues or biofluids related to obesity-associated OA. We describe relevant studies and discuss challenges studying obesity as a disease-related factor in OA. ResultsOf the 107 publications identified by our search criteria, only 15 specifically used transcriptomics or metabolomics to study joint tissues or biofluids in obesity-related OA. Specific transcriptomic and metabolomic signatures associated with obesity-related OA have been defined in select local joint tissues, biofluids and other biological material. However, considerable challenges exist in understanding contributions of obesity-associated modifications of transcriptomes and metabolomes related to OA, including sociodemographic, anthropometric, dietary and molecular redundancy-related factors. ConclusionsA number of additional transcriptomic and metabolomic studies are needed to comprehensively understand how obesity affects OA incidence, progression and outcomes. Integration of transcriptome and metabolome signatures from multiple tissues and biofluids, using network-based approaches will likely help to better define putative therapeutic targets that could enable precision medicine approaches to obese OA patients.

Modular Approach to Highly Substituted 3-Methylpyridones.

A method has been developed for the rapid synthesis of highly substituted 3-methylpyridones via the condensation of Baylis-Hillman amines and ketones under benzoic acid catalysis. The process features readily available starting materials, broad substrate scope, high functional group tolerance, excellent regioselectivity, and gram-scale synthesis. We envision that this on-demand construction of 3-methylpyridones will provide exciting opportunities in biological research, therapeutics, and material sciences.

Spider silk biological material for Q-switched temperature sensor

Abstract A temperature sensor using compact design and highly sensitivity of side polished fiber and fiber Bragg grating as the sensing elements, Q-switched pulse fiber laser source with spider silk as a saturable absorber is proposed and demonstrated. Spider silk sample was gently collected from a live spider, specifically, the jumping spider of Plexippus sp. which then incorporated within the laser cavity by deposited the silk onto the surface of the fiber ferrule to facilitate the generation of Q-switched pulse fiber laser. The temperature variations were detected by monitoring the pulse train and radio frequency shift from the oscilloscope. The performance of the side polished fiber sensor probe shows a sensitivity of 0.1522 kHz/°C, with 0.9479 coefficient of determination value as the temperature increased from -0.5 °C to +3.1 °C. Besides, a linear temperature re-sponse in the range of 25 °C – 55 °C with a sensitivity of 0.0423 kHz/°C, and a linear correlation coefficient of 0.951 was experimentally achieved for a fiber Bragg grating device. The spider silk as a saturable absorber material is compatible with fiber optic interconnection and the temperature sensing characteristics were successfully demonstrated. The sensor's straight-forward design further enhances its desirability as a sensor for temperature monitoring, including in the field of biological treatments, consumer electronics, detection of chemical analytes, and medical diagnosis.

Abstract PO2-20-05: Onco-Genome Brazil: Mapping Breast and Prostate Cancer in the Brazilian Public Health System

Abstract Background: Breast and prostate cancers are the most common malignancies diagnosed in women and men respectively, and present with great clinical heterogeneity, even in tumors with the same phenotypic characteristics. Somatic and germline molecular alterations in DNA may have prognostic and predictive impact, influencing response to therapies and overall survival. In addition, the evaluation of germline mutations can help identify individuals and families at higher risk for developing cancer. Aims: Our aim is to characterize the somatic and germline genomic landscape of women with locally advanced HER2-positive breast cancer and men with metastatic prostate cancer from Brazil. Secondarily, we aim to identify genetic variants associated with tumor prognosis and treatment response, identify patients carrying pathogenic alterations in cancer-predisposing genes, and characterize the genetic ancestry of the population included in the study. Trial design: This observational multicenter cohort study (NCT05306600) will include 550 adult patients from the five macro-regions of Brazil, divided into two arms: 1) breast cancer and 2) prostate cancer. Clinical and pathological data will be collected, as well as DNA samples from peripheral blood and tumor tissue. Whole-exome sequencing (WES) will be performed to identify variants that may be drivers and/or actionable in a specific patient or tumor. These variants will be interpreted and classified according to their population frequencies, in silico predictors, functional studies, and literature data, following international guidelines proposed by expert societies. This trial is supported by the Ministry of Health in Brazil and includes patients of the Public Health System. Eligibility criteria: In arm 1, the inclusion criteria are patients with a histological diagnosis of breast carcinoma with overexpression of HER-2, clinical stage II or III, and undergoing neoadjuvant treatment with chemotherapy plus trastuzumab. In arm 2, the criteria are patient with histological diagnosis of prostate adenocarcinoma, currently in clinical stage IV. Patients without availability of biological material collection are excluded from the study, as well as patients in whom there was no central confirmation of required histology. Statistical methods: Univariate and multivariate analyses will be conducted to evaluate the possible effect of specific genes or mutations on the investigated outcomes, including tumor prognosis and treatment response. Discussion: Currently, 265 participants have already been included in the study, 150 in arm 1 and 115 in arm 2. This trial will contribute to the construction of a robust database that should provide a better understanding of the genomic profile of patients with breast and prostate cancer in Brazil. For more information about the trial, please contact Daniela Rosa (daniela.rosa@hmv.org.br). Citation Format: Jaqueline Schuch, Cláudia Bordignon, Mahira Rosa, Angélica de Baumont, Marina Bessel, Gabriel Macedo, Daniela Rosa. Onco-Genome Brazil: Mapping Breast and Prostate Cancer in the Brazilian Public Health System [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-20-05.