Graph theory, a branch of mathematics that focuses on the study of graphs (networks of nodes and edges), provides a robust framework for analysing the structural and functional properties of biomolecules. By leveraging molecular dynamics (MD) simulations, atoms or groups of atoms can be represented as nodes, while their dynamic interactions are depicted as edges. This network-based approach facilitates the characterization of properties such as connectivity, centrality, and modularity, which are essential for understanding the behaviour of molecular systems. This review details the application and development of graph theory-based models in studying biomolecular systems. We introduce key concepts in graph theory and demonstrate their practical applications, illustrating how innovative graph theory approaches can be employed to design biomolecular systems with enhanced functionality. Specifically, we explore the integration of graph theoretical methods with MD simulations to gain deeper insights into complex biological phenomena, such as allosteric regulation, conformational dynamics, and catalytic functions. Ultimately, graph theory has proven to be a powerful tool in the field of molecular dynamics, offering valuable insights into the structural properties, dynamics, and interactions of molecular systems. This review establishes a foundation for using graph theory in molecular design and engineering, highlighting its potential to transform the field and drive advancements in the understanding and manipulation of biomolecular systems.

Phosphate in the form of organic compounds can be bound in soils containing the aluminosilicate allophane. A significant part of this phosphorus is believed to be present as nucleic acids. The interaction of yeast RNA with allophane was studied to further the understanding of the allophane/organic macro molecule interaction as well as the binding of organic phosphorus by allophanic soils. The extent of RNA adsorption on the allophane was dependent upon the pH, the charge and concentration of simple cations, the concentration of RNA, and the time of interaction. From a mixture containing 145 mg/liter RNA and 2.9 g/liter allophane in 10−2 M NaCl, the amount of RNA adsorbed increased from 6% at pH 10 to 98% at pH 3. The adsorption also increased as the concentration of added NaCl was increased from 10−4 M to 10−1 M, but only when the pH was greater than 5, i.e., above the isoelectric point of the clay. Mg2+ and Ca2+ were equally much more effective at promoting adsorption than Na+ at the same concentrations. There was no difference in the effectiveness of SO4−2, Cl−, or NO3− at pH 5 or higher. The adsorption isotherm at pH 7 can be described by the Langmuir equation; the apparent adsorption maximum was 38 mg/g. Van der Waals and simple electrostatic forces appear to dominate the interaction leading to the adsorption of RNA by allophane.

This study aimed to assess the prevalence of anti-hepatitis E virus (HEV) immunoglobulin (Ig) M and elevated serum alanine aminotransferase (ALT) levels among employees in catering and public place industries. Blood samples were collected between January and December 2020 from 26,790 employees working in the Qinhuai district of Nanjing, China. Anti-HEV IgM in the serum samples was tested by the capture ELISA method and ALT was tested by the IFCC method. Samples positive for anti-HEV IgM or with ALT levels over 200 U/L were subjected to PCR screening of HEV RNA. The overall seroprevalence of anti-HEV IgM was 0.41%, and the seroprevalence was slightly higher in males (0.47%) than in females (0.37%); however, the difference was not substantial (p = 0.177). Seroprevalence of anti-HEV IgM increased with age, reaching its peak level after 48 years of age. The prevalence of elevated ALT levels was 4.24%, and males exhibited a higher prevalence than females (6.78% vs 2.65%, p < 0.001). Prevalence of elevated ALT levels differed in age groups and the 26–36-year-old group had the highest rate of elevated ALT levels. Employees with elevated ALT levels had a higher prevalence of positive anti-HEV IgM than those with normal ALT (0.57% vs 0.31%, p < 0.001). Positive HEV RNA was detected in one anti-HEV IgM-negative employee with ALT higher than 200 U/L. In our study, all the HEV RNA-positive and IgM-positive individuals are asymptomatic, and a combination of ALT tests, serological methods, and molecular methods is recommended to screen asymptomatic HEV carriers and reduce the risk of transmission.

DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general ‘rules’ that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.

The purpose of this study was to investigate potential mechanisms involved in fat deposition promoted by dietary lysine deficiency, particularly intramuscular fat (IMF), and differential responses between fatty and lean pigs. Carcass traits and lipogenic enzyme activities and gene expression levels in muscles and adipose tissue were investigated in Iberian (fatty) and Landrace × Large White (LDW) pigs under identical feeding level (based on body weight (BW)) and management conditions. Twenty-eight barrows of 10 kg initial BW, 14 per breed, were fed two isoproteic (200 g CP /kg DM) and isocaloric (14.7 MJ metabolizable energy/kg DM) diets with identical composition except for the lysine content (1.09% for diet adequate in lysine and 0.52% for diet deficient in lysine). At a BW of 25 kg, pigs were slaughtered. Compared with pigs fed the lysine-adequate diet, in both genotypes lysine-deficient diet led to lower carcass protein concentration, lower relative proportions of leaner components (loin, ham and shoulder; P < 0.01), and higher carcass fatty components and carcass lipid concentration (P < 0.001). Irrespective of diet, the activity and gene expression of lipogenic enzymes (fatty acid synthase (FAS), malic enzyme (ME) and glucose-6-phosphate dehydrogenase (G6PDH)) were greater in Iberian than in LDW pigs, particularly in adipose tissue where transcriptional regulators involved in the control of adipogenesis and lipogenesis were also upregulated in Iberian animals. In backfat tissue, there was a small decrease induced by or no effects of lysine-deficient diet on the activity and gene expression of lipogenic enzymes, nor in gene expression levels of upstream regulators of lipogenesis and adipogenesis. In longissimus muscle, the activity of FAS, G6PDH and ME increased with lysine deficiency in both genotypes (P < 0.01) and an upregulation of gene expression of lipogenic enzymes was specifically observed in Iberian pigs (P < 0.05 to P < 0.001). In biceps femoris muscle of lysine-deficient pigs, the activity of FAS and ME enzymes increased, ME1 gene was upregulated (added to FASN gene in the case of Iberian pigs; P < 0.01 to P < 0.001) and PPARA gene was downregulated (P < 0.05). The results show that in both fatty and lean pigs, the effect of lysine deficiency on lipid metabolism was tissue-specific, with an activation of lipogenesis in longissimus and biceps femoris muscle but no apparent stimulation in backfat adipose tissue. Suitable feeding protocols including lysine-deficient diets should be designed for each pig type in order to increase intramuscular lipids without penalizing the growth of lean carcass components.

The effects of sethoxydim {2-[1-(ethoxyimino) butyl]-5-[2-(ethylthio)propyl]-3-hydroxy-2-cyclohexen-1-one} on the metabolic activity of excised root tips of corn (Zea mays, L. ‘Goldencrossbantam′) were studied under laboratory conditions. Uptake and incorporation of 14C-labeled thymidine, uridine, leucine, glucose, and acetic acid into cell constituents, as well as respiration, increased continuously with time progressions during the incubation period. Sethoxydim did not affect either the uptake of any 14C-precursor into or respiration of the root tip tissue. Although RNA and protein syntheses were not affected by the herbicide, DNA and cell wall syntheses were inhibited 120 min after treatment with sethoxydim. Incorporation of 14C-acetic acid into lipid fraction was inhibited by sethoxydim in a time- and concentration-dependent fashion. This inhibition was observed at a shorter time after sethoxydim treatment than that of any other 14C-precursor. The effect was not observed in the nonproliferative regions of corn roots, whereas cerulenin (a fatty acid synthase inhibitor) inhibited the incorporation of 14C-acetic acid both in proliferative and nonproliferative regions. It is suggested that the inhibition of lipid synthesis by sethoxydim does not play a major role in the mode of action of this herbicide. The effects of sethoxydim, including those on lipid metabolism, are closely associated with proliferative conditions of susceptible graminaceous plants.

Suspension cultures of proso millet cells were treated with haloxyfop at different phases of growth. Treatment of 1-d cultures with 1 μM haloxyfop completely inhibited growth within 48 h. In contrast, 1 mM haloxyfop was required to elicit a similar response in 4-, 7-, or 10-d cultures. Calculated IC50 values indicated a 300-fold decrease in haloxyfop sensitivity during the period from 1 to 4 d. The observed changes in sensitivity to haloxyfop could not be attributed to changes in cell concentration during culture growth. In both 1-d and 4-d cultures, an initial rapid uptake of radiolabel was followed by a slow loss of radiolabel from cells. Almost all radioactivity extracted from 1-d and 4-d cells was present as the parent acid. Several radiolabeled compounds in addition to the parent acid were present in media. No major differences in the amounts of these materials were found between 1-d and 4-d media. Our results indicate that a special aspect of metabolism expressed during cell division is particularly sensitive to the herbicide.

Dark-incubated common purslane (Portulaca oleracea L.) seed synthesize very little protein and essentially no nucleic acids. Dark-incubated seed incorporate only 14 × 10−3 nmoles 14C-leucine/mg protein/12-h dark. In contrast, seed exposed to 12-h light following 24-h dark incubation incorporate 365 × 10−3-nmoles 14C-leucine/mg protein/12-h light. Once dormancy is broken by exposure of seed to light, initiation of radicle protrusion occurs at 12 h. Protein synthesis gradually increases with time in the light and precedes nucleic acid synthesis which is associated with radicle protrusion. During the 12-h lag period preceding radicle protrusion protein synthesis increases significantly by 3 to 9 h in light, RNA synthesis by 9 h in light, and DNA synthesis by 12 h in light. After 12 h in light, 32P can be detected in all nucleic acid fractions, DNA and RNAs.

The cat flea, Ctenocephalides felis, is a major pest species on companion animals thus of significant importance to the animal health industry. The aim of this study was to develop sampling and storage protocols and identify stable reference genes for gene expression studies to fully utilize the growing body of molecular knowledge of C. felis. RNA integrity was assessed in adult and larvae samples, which were either pierced or not pierced and stored in RNAlater at ambient temperature. RNA quality was maintained best in pierced samples, with negligible degradation evident after 10 days. RNA quality from non-pierced samples was poor within 3 days. Ten candidate reference genes were evaluated for their stability across four group comparisons (developmental stages, genders, feeding statuses and insecticide-treatment statuses). Glyceraldehyde 3 phosphate dehydrogenase (GAPDH), 60S ribosomal protein L19 (RPL19) and elongation factor-1α (Ef) were ranked highly in all stability comparisons, thus are recommended as reference genes under similar conditions. Employing just two of these three stable reference genes was sufficient for accurate normalization. Our results make a significant contribution to the future of gene expression studies in C. felis, describing validated sample preparation procedures and reference genes for use in this common pest.

In the present work, it is shown that thermodynamically feasible polymerization of cyanomethanol, which can be formed from formaldehyde and hydrogen cyanide, can lead to synthesis of polypeptides as well as to the previously reported synthesis of RNA. If the polymerization takes place on a one-dimensional feature of a mineral, such as for example a crack on its surface, the concept of quasi-chirality is introduced to describe the adsorbed polypeptide. This, in principle, would lead to formation of proteins that are completely homochiral in their alpha carbon groups. The concept of quasi-chirality can also be introduced in the condensation of glycine under similar conditions to form a polypeptide. This again leads to proteins completely chiral in their alpha carbon groups.

Leishmaniasis development is multifactorial; nonetheless, the establishment of the infection, which occurs by the survival and replication of the parasite inside its main host cell, the macrophage, is mandatory. Thus, the importance of studying the molecular mechanisms involved in the Leishmania–macrophage interaction is highlighted. The aim of this study was to characterize a cellular model of macrophages derived from U937 cells that would allow for the identification of infection phenotypes induced by genetic silencing with interference RNA in the context of macrophages infected with Leishmania (Viannia) braziliensis. The model was standardized by silencing an exogenous gene (gfp), an endogenous gene (lmna) and a differentially expressed gene between infected and non-infected macrophages (gro-β). The silencing process was successful for the three genes studied, obtaining reductions of 88·9% in the GFP levels, 87·5% in LMNA levels and 74·4% for Gro-β with respect to the corresponding control cell lines. The cell model revealed changes in the infection phenotype of the macrophages in terms of number of amastigotes per infected macrophage, number of amastigotes per sampled macrophage and percentage of infected macrophages as a result of gene silencing. Thus, this cell model constitutes a research platform for the study of parasite–host interactions and for the identification of potentially therapeutic targets.

Careful examination of the present metabolism and in vitro selection of various catalytic RNAs strongly support the RNA world hypothesis as a crucial step of the origins and early life evolution. Small functional RNAs were exposed from 10 March 2009 to 21 January 2011 to space conditions on board the International Space Station in the EXPOSE-R mission. The aim of this study was to investigate the preservation or modification properties such as integrity of RNAs after space exposition. The exposition to the solar radiation has a strong degradation effect on the size distribution of RNA. Moreover, the comparison between the in-flight samples, exposed to the Sun and not exposed, indicates that the solar radiation degrades RNA bases.

In 2004 the Netherlands Twin Register (NTR) started a large scale biological sample collection in twin families to create a resource for genetic studies on health, lifestyle and personality. Between January 2004 and July 2008, adult participants from NTR research projects were invited into the study. During a home visit between 7:00 and 10:00 am, fasting blood and morning urine samples were collected. Fertile women were bled on day 2–4 of the menstrual cycle, or in their pill-free week. Biological samples were collected for DNA isolation, gene expression studies, creation of cell lines and for biomarker assessment. At the time of blood sampling, additional phenotypic information concerning health, medication use, body composition and smoking was collected. Of the participants contacted, 69% participated. Blood and urine samples were collected in 9,530 participants (63% female, average age 44.4 (SD 15.5) years) from 3,477 families. Lipid profile, glucose, insulin, HbA1c, haematology, CRP, fibrinogen, liver enzymes and creatinine have been assessed. Longitudinal survey data on health, personality and lifestyle are currently available for 90% of all participants. Genome-wide SNP data are available for 3,524 participants, with additional genotyping ongoing. The NTR biobank, combined with the extensive phenotypic information available within the NTR, provides a valuable resource for the study of genetic determinants of individual differences in mental and physical health. It offers opportunities for DNA-based and gene expression studies as well as for future metabolomic and proteomic projects.