Hasil untuk "Biology (General)"

K. Queiroz

M. Rosenberg

B. Perthame

K. Jaeger, B. Dijkstra, M. Reetz

Mary C. Thomas, C. Chiang

L. Allen

M. Cichorek, M. Wachulska, Aneta Stasiewicz et al.

In the human skin, melanocytes are present in the epidermis and hair follicles. The basic features of these cells are the ability to melanin production and the origin from neural crest cells. This last element is important because there are other cells able to produce melanin but of different embryonic origin (pigmented epithelium of retina, some neurons, adipocytes). The life cycle of melanocyte consists of several steps including differentiation of melanocyte lineage/s from neural crest, migration and proliferation of melanoblasts, differentiation of melanoblasts into melanocytes, proliferation and maturation of melanocytes at the target places (activity of melanogenic enzymes, melanosome formation and transport to keratinocytes) and eventual cell death (hair melanocytes). Melanocytes of the epidermis and hair are cells sharing some common features but in general they form biologically different populations living in unique niches of the skin.

Nghia Nhu Nguyen, Bao The Nguyen, Huyen Thi Ngoc Le et al.

Background Liver fibrosis is a significant health burden in Vietnamese male adults, driven by high rates of hepatitis B and hepatitis C, excessive alcohol consumption, and genetic and environmental factors. Despite progress in diagnostic tools, there is a pressing need for cost-effective screening methods tailored to this high-risk group, particularly in resource-limited settings. Methods This study enrolled 952 Vietnamese male adults over 40 years old undergoing FibroScan, excluding those with conditions affecting test accuracy. Data on demographics, clinical history, and anthropometrics were collected, and fibrosis stages were classified using the METAVIR system. Model development combined Bayesian model averaging and forward stepwise methods, with predictive performance validated via receiver operating characteristic (ROC) analysis and area under the curve (AUC) estimation in the R environment. Results Among 952 male participants, the prevalence of liver fibrosis was 19.9%, with most cases classified as mild (F1). Multivariate analysis identified significant risk factors, including advanced age (odds ratio (OR) = 1.6; 95% confidence interval (CI) [1.02–2.51]), alcohol abuse (OR = 4.44; 95% CI [2.65–7.42]), hepatitis B (OR = 6.76; 95% CI [3.14–14.54], hepatitis C (OR = 33.04; 95% CI [5.26–207.42]), family history of cirrhosis (OR = 16.14; 95% CI [3.28–79.55]), and hepatic steatosis (OR = 4.02; 95% CI [2.57–6.28]). The predictive model demonstrated good discriminative performance with an AUC of 0.769 (95% CI [0.734–0.800]) and showed satisfactory calibration through bootstrap resampling, indicating close agreement between predicted and observed risks. Conclusion The current prevalence of liver fibrosis among Vietnamese male adults was found to be 19.9%, and the developed risk prediction model effectively identifies high-risk individuals, enabling early diagnosis and targeted prevention, particularly in resource-limited settings. However, the lack of external validation and the sample restricted to Vietnamese male adults limit the generalizability of the model, which should be further evaluated in other populations.

Connor McShaffrey, Eran Agmon, Randall D. Beer

Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a principled understanding of how cellular dynamics interact with them and how they originate in actual biology. Computational cell biology will only overcome these concerns once it treats the life-death boundary as a central concept, creating a theory of cellular viability. We lay the foundation for such a development by demonstrating how specific geometric structures can separate regions of qualitatively similar survival outcomes in our models, offering new global organizing principles for cell fate. We also argue that idealized models of emergent individuals offer a tractable way to begin understanding life's intrinsically generated limits.

Lukas Buecherl, Felipe X. Buson, Georgie Hau Sørensen et al.

Standards play a crucial role in ensuring consistency, interoperability, and efficiency of communication across various disciplines. In the field of synthetic biology, the Synthetic Biology Open Language (SBOL) Visual standard was introduced in 2013 to establish a structured framework for visually representing genetic designs. Over the past decade, SBOL Visual has evolved from a simple set of 21 glyphs into a comprehensive diagrammatic language for biological designs. This perspective reflects on the first ten years of SBOL Visual, tracing its evolution from inception to version 3.0. We examine the standard's adoption over time, highlighting its growing use in scientific publications, the development of supporting visualization tools, and ongoing efforts to enhance clarity and accessibility in communicating genetic design information. While trends in adoption show steady increases, achieving full compliance and use of best practices will require additional efforts. Looking ahead, the continued refinement of SBOL Visual and broader community engagement will be essential to ensuring its long-term value as the field of synthetic biology develops.

Lee A. Bulla

Bioinsecticides based on the bacterium <i>Bacillus thuringiensis</i> (Bt) are widely used as safe alternatives to chemical insecticides. The insecticidal activity of Bt is occasioned by a protein toxin contained in parasporal crystals (Cry proteins) that are synthesized and laid down alongside the endospore during sporulation. The specificity of toxin action is associated with the subspecies of Bt and the individual Cry toxins they produce. Although a number of commercial Bt formulations are available to control moths, mosquitoes and beetles, there are none that control the red imported fire ant (RIFA) <i>Solenopsis invicta</i>. The present report is the first to describe the insecticidal activity of the Cry3A protein toxin, produced by <i>Bacillus thuringiensis</i> subsp. <i>tenebrionis</i> (Btt), against the RIFA as well as some of its key biochemical properties. Currently available commercial formulations of Btt are designed to control beetles such as the Colorado potato beetle, not ants. The Cry3A toxin (MW ~66 kDa) is embedded in a larger polypeptide (protoxin, MW ~73 kDa) and is released from the toxin enzymatically. Once activated, it can be administered to the RIFA as a soluble protein that most likely binds to an attendant receptor in the epithelial cells that line the wall of the larval ventriculus, killing the insect. Properly customized, the Cry3A toxin is a potential candidate for fire ant control.

Alex Ferreira da Silva, Franciele Jesus Lima, Alyne Riani Moreira et al.

Aberrant Rho-associated kinase function could be associated with increased bone fragility. Since cigarette smoke (CS) exposure promotes the increase in bone fragility due to changes in bone tissue components, this study aimed to investigate how CS exposure could modulate the Rho kinase-associated bone structural changes. Mice were assigned to four groups: control; smoke; control with Rho kinase inhibitor administration; and smoke with a Rho kinase inhibitor. Bone samples were obtained to assess bone histomorphometry analysis, type I collagen composition, and MEPE expression in trabeculae. We observed that CS exposure induced decreased trabecular and osteoid thickness. A concomitant increase in the osteoclastic and erosion surfaces and a decrease in the mineralization surface were observed. Additionally, CS exposure decreased the type I collagen and MEPE expression. Rho kinase inhibitor administration recovered the bone mineralization and the collagen type I deposition. Conclusions: CS exposure increases Rho kinase activity in bone cells, leading to structural changes. The administration of a Rho GTPases inhibitor partially reverses these effects, likely due to the recovery in osteoblast activity.

Yutaro Hama, Yuko Fujioka, Hayashi Yamamoto et al.

In mammals, autophagosome formation, a central event in autophagy, is initiated by the ULK complex comprising ULK1/2, FIP200, ATG13, and ATG101. However, the structural basis and mechanism underlying the ULK complex assembly have yet to be fully clarified. Here, we predicted the core interactions organizing the ULK complex using AlphaFold, which proposed that the intrinsically disordered region of ATG13 engages the bases of the two UBL domains in the FIP200 dimer via two phenylalanines and also binds the tandem microtubule-interacting and transport domain of ULK1, thereby yielding the 1:1:2 stoichiometry of the ULK1–ATG13–FIP200 complex. We validated the predicted interactions by point mutations and demonstrated direct triad interactions among ULK1, ATG13, and FIP200 in vitro and in cells, wherein each interaction was additively important for autophagic flux. These results indicate that the ULK1–ATG13–FIP200 triadic interaction is crucial for autophagosome formation and provides a structural basis and insights into the regulation mechanism of autophagy initiation in mammals.

Chun-Hua Wang, Lu-Kai Wang, Fu-Ming Tsai

Tazarotene, a retinoid derivative, is widely used in treating skin conditions such as psoriasis and acne. Recent studies have demonstrated its potential as a promising therapeutic agent for treating melanoma in situ. Its primary mechanism of action involves the selective activation of retinoic acid receptors (RAR-β and RAR-γ), which play important roles in regulating cell growth, differentiation, and apoptosis. By activating these receptors, tazarotene influences the expression of several downstream inducible genes, such as tazarotene-induced gene-1 (<i>TIG1</i>), <i>TIG2</i>, and <i>TIG3</i>. These genes play crucial roles in regulating melanoma cell proliferation, invasiveness, and immune responses in the tumor microenvironment. This review aims to provide a comprehensive overview of the current status of retinoid derivatives—particularly tazarotene—in melanoma treatment and the latest research regarding their molecular mechanisms. We will explore how tazarotene suppresses melanoma growth through gene regulation mechanisms and discuss its potential role in immune responses within the tumor microenvironment. Additionally, we assess the advantages and challenges of using tazarotene as a topical treatment and explore its future clinical applications. These studies contribute to a wider understanding of tazarotene’s antitumor mechanisms, providing a solid theoretical foundation for its potential as a therapeutic option for melanoma in situ.

Yuanchen Cheng, Zichen Zhang, Yuqing Liu et al.

Accurate estimation of tuna catch is crucial for effective pelagic fishery management and resource conservation. However, existing manual counting methods suffer from issues such as low accuracy and poor timeliness, highlighting the urgent need for an efficient and automated solution. This paper proposes an automatic tuna counting method based on the YOLOv8n-DMTNet target detection algorithm combined with the improved ByteTrack tracking algorithm. The method uses YOLOv8n as the base model, enhanced with detail-enhanced convolution and a multi-scale feature fusion pyramid network, which significantly improves detection accuracy in complex marine environments. Additionally, a dynamic, task-aligned detection head is introduced to optimize the synergy between classification and localization tasks. To further improve counting accuracy, the ByteTrack algorithm is employed for target tracking, and a region-specific counting method is designed to prevent double counting and omission due to occlusion and motion irregularities. Experimental results show that the improved YOLOv8n-DMTNet model achieves a 9.2% increase in mAP@0.5 and a 6.4% increase in mAP@0.5:0.95 compared to YOLOv8n in the tuna detection task, while reducing the number of parameters by 42.3% and computational complexity by 33.3%. The counting accuracy reaches 93.5%, and the method demonstrates superior performance in terms of accuracy, robustness, and computational resource efficiency, making it well-suited for resource-constrained fishing vessel environments. This approach provides reliable technical support for automated catch counting in pelagic fisheries.

Longfei Cui, Xinyu Niu, Haizhong Qian et al.

The extraction of shape features from vector elements is essential in cartography and geographic information science, supporting a range of intelligent processing tasks. Traditional methods rely on different machine learning algorithms tailored to specific types of line and polygon elements, limiting their general applicability. This study introduces a novel approach called “Pre-Trained Shape Feature Representations from Transformers (PSRT)”, which utilizes transformer encoders designed with three self-supervised pre-training tasks: coordinate masking prediction, coordinate offset correction, and coordinate sequence rearrangement. This approach enables the extraction of general shape features applicable to both line and polygon elements, generating high-dimensional embedded feature vectors. These vectors facilitate downstream tasks like shape classification, pattern recognition, and cartographic generalization. Our experimental results show that PSRT can extract vector shape features effectively without needing labeled samples and is adaptable to various types of vector features. Compared to the methods without pre-training, PSRT enhances training efficiency by over five times and improves accuracy by 5–10% in tasks such as line element matching and polygon shape classification. This innovative approach offers a more unified, efficient solution for processing vector shape data across different applications.

Richard J. Abdill, Emma Talarico, Laura Grieneisen

Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities for discovery even outside of the much-discussed developments in artificial intelligence. However, guidance for implementing these techniques is much easier to find than guidance for reporting their use, leaving biologists to guess which details and files are relevant. Here, we provide a set of recommendations for sharing code, with an eye toward guiding those who are comparatively new to applying open science principles to their computational work. Additionally, we review existing literature on the topic, summarize the most common tips, and evaluate the code-sharing policies of the most influential journals in biology, which occasionally encourage code-sharing but seldom require it. Taken together, we provide a user manual for biologists who seek to follow code-sharing best practices but are unsure where to start.

Diana T. Pham, Zdzislaw E. Musielak

The Lagrangian formalism has attracted the attention of mathematicians and physicists for more than 250 years and has played significant roles in establishing modern theoretical physics. The history of the Lagrangian formalism in biology is much shorter, spanning only the last 50 years. In this paper, a broad review of the Lagrangian formalism in biology is presented in the context of both its historical and modern developments. Detailed descriptions of different methods to derive Lagrangians for five selected population dynamics models are given and the resulting Lagrangians are presented and discussed. The procedure to use the obtained Lagrangians to gain new biological insights into the evolution of the populations without solving the equations of motion is described and applied to the models. Finally, perspectives of the Lagrangian formalism in biology are discussed.

Lui Ng, Sunny Kit-Man Wong, Hung-Sing Li et al.

Background: The dysregulation of gene expression is one of the key molecular features of colorectal cancer (CRC) development. This study aimed to investigate whether such dysregulation is reflected in rectal swab specimens of CRC patients and to evaluate its potential as a non-invasive approach for screening. Methods: We compared the expression level of 14 CRC-associated genes in tumor and adjacent non-tumor tissue of CRC patients and examined the correlation of their levels in tissue with paired rectal swab specimens. The level of these 14 genes in rectal swab specimens was compared among patients with CRC or polyp and control subjects, and the diagnostic potential of each dysregulated gene and the gene panel were evaluated. Results: The expression of <i>CXCR2</i>, <i>SAA</i>, <i>COX1</i>, <i>PPARδ</i>, <i>PPARγ</i>, <i>Groγ</i>, <i>IL8</i>, <i>p21</i>, <i>c-myc</i>, <i>CD44</i> and <i>CSF1</i> was significantly higher in CRC, and there was a significant correlation in the levels of most of them between the CRC and rectal swab specimens. In the training study, we showed that <i>CD44</i>, <i>IL8</i>, <i>CXCR2</i> and <i>c-myc</i> levels were significantly higher in the rectal swab specimens of the CRC patients. Such result was confirmed in the validation study. A panel of these four genes was developed, and ROC analysis showed that this four-gene panel could identify CRC patients with an AUC value of 0.83 and identify overall polyp and precancerous adenoma patients with AUC values of 0.6522 and 0.7322, respectively. Finally, the predictive study showed that the four-gene panel demonstrated sensitivities of 63.6%, 76.9% and 88.9% in identifying overall polyp, precancerous adenoma and CRC patients, respectively, whereas the specificity for normal subjects was 72.2%. Conclusion: The expression of CRC-associated genes in rectal swab specimens reflects the dysregulation status in colorectal tissue, and the four-gene panel is a potential non-invasive biomarker for early precancerous adenoma and CRC screening.

Majed Alluqmani, Abdulfatah M. Alayoubi, Jamil A. Hashmi et al.

BackgroundVariants in a gene encoding sodium voltage-gated channel alpha subunit 1 (SCN1A) are known to cause a broad clinical spectrum of epilepsy and associated features, including Dravet syndrome (MIM 607208), non-Dravet developmental and epileptic encephalopathy (MIM 619317), familial febrile seizures (MIM 604403), familial hemiplegic migraine (MIM 609634), and generalized epilepsy with febrile seizures (MIM 604403).MethodsIn this study, we examined a patient with Parkinson’s disease (PD) without any clinical manifestations of epilepsy and associated features. Genomic nucleic acid was extracted, and a complete coding sequence of the human genome (whole-exome sequencing) was sequenced. Moreover, Sanger sequencing of variants of interest was performed to validate the exome-discovered variants.ResultsWe identified a heterozygous pathogenic missense mutation (c.1498C&gt;T; p.Arg500Trp) in the SCN1A gene in the patient using the whole-exome sequencing approach. The onset of PD features in our patient occurred at the age of 30 years. Biochemical investigations were carried out to rule out any secondary cause of the disease, including Wilson's disease or another metabolic disorder. MRI of the brain and spinal images were unremarkable. Moreover, a dramatic response to carbidopa–levodopa treatment was also observed in the patient.ConclusionOur results suggest that the pathogenic variant in SCN1A may lead to PD features without epilepsy.