Internal Region Research Articles

Glucuronic acid: not just another brick in the cell wall.

This article is a Commentary on Debra‐Maceluch et al. (2023), 238: 297–312.

Abstract P3-07-27: In vitro antitumoral activity of endophytic fungi isolated from Lophocereus marginatus against the human breast cancer cell line MCF-7

Abstract Breast cancer is the most frequent malignant tumor among women and is the leading cause of death from cancer worldwide. In 2020, 90,222 deaths from breast cancer were reported in México. However, cancer cells resistant to antineoplastic drugs are frequent, which compromises the patient’s survival. For this reason, in oncology, it is essential to search for new sources of anticancer compounds. Endophytic fungi are currently considered potential reservoirs for compounds with antitumor activity. More than 100 different classes of secondary metabolites have been reported with activity against different types of cancer, including breast cancer. Therefore, the objective of this study was to evaluate the activity of methanol extracts of endophytic fungi isolated from Lophocereus marginatus against the MCF-7 breast cancer cell line, using as controls the MA-104 cell line human peripheral blood mononuclear cells. Fungal strains were isolated from stems of L. marginatus and molecularly identified from ribosomal DNA internal transcript spacer region sequencing. Extraction of the secondary metabolites was performed from the maceration of mycelium fungus in methanol. The solvent was removed with a rotary evaporator and the extract was reconstituted with dimethyl sulfoxide (DMSO). Next, cells were incubated with the extract at concentrations ranging from 31.25 µg/mL to 250 µg/mL for 48 h at 37 °C and 5% CO2. Growth inhibition was assessed by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide reduction assay, using 1% DMSO was used as a negative control. IC50 values and selectivity indexes (SI) were then calculated. It was found that tumor cells growth inhibition by the extracts increased in a concentration-dependent manner. A. versicolor PME-H005 strain extract showed the highest antitumor activity, with up to 58.9% growth inhibition at 250 µg/mL and IC50 value of 95.21 ± 1 µg/mL against MCF-7 cells. The highest SI was obtained with MCF-7 cell s with 2.77, as compared with normal PBMC with an IC50 of 264 ± 1.5 µg/mL. In addition, the M. anisopliae PME-H007 strain presented a high SI value of 2.1 and an IC50 of 245.9 ± 1.9 µg/mL, using the MCF-7 cell line. This study shows the potential of the endophytic fungus A. versicolor PME-H005 isolated from L. marginatus for production of secondary metabolites with antitumor activity against MCF-7 cells. Citation Format: Jesica M. Ramírez Villalobos, Cesar I. Romo Sáenz, Karla S. Morán Santibañez, Patricia Tamez Guerra, Orquídea Pérez González, Reyes Tamez Guerra, Cristina Rodríguez-Padilla, Ricardo A. Gomez Flores. In vitro antitumoral activity of endophytic fungi isolated from Lophocereus marginatus against the human breast cancer cell line MCF-7 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-07-27.

Tutorial on vibration and sound

Over the years I have written many tutorials on vibroacoustics. This tutorial summarizes much of the material in those articles, starting with structural flexural vibrations and how they radiate sound. I explain structural modes of vibration, how they sum into structural mobilities, and how to use infinite plate theory to estimate the means of those mobilities. I also show that as structural damping increases, the mobilities of finite structures converge to that of an infinite structure. Next, you will see how structural flexural waves radiate sound into adjacent acoustic spaces. The radiated sound power may be normalized to a nondimensional radiation efficiency. Next we will examine fluid loading effects on structures, including loading from exterior and internal acoustic regions. I will show how exterior heavy fluid loading (from water) significantly mass loads and radiation damps structural vibrations. I will also show how internal air cavities can stiffen low order structural modes, and in some cases cause coupled oscillator behavior when structural and cavity mode resonance frequencies coincide. Finally, I will explore the fundamentals of sound transmission loss through structural barriers. My complete tutorial series on vibroacoustics is available at hambricacoustics.com.

Isolation of Streptomycin-Resistant Erwinia pyrifoliae in Korea.

As a black shoot blight disease-causing agent, Erwinia pyrifoliae was first reported in 1995 in Korea. A total of 101 isolates of E. pyrifoliae were isolated from samples showing bacterial symptoms collected from apple and pear orchards between 2020 and 2021. These isolates were screened for streptomycin resistance, with one from an orchard in Gwangju showing resistance at 100 μg/ml streptomycin. This streptomycin-resistant E. pyrifoliae (EpSmR) isolate was identified via polymerase chain reaction amplification of the strA/strB gene and an internal region of the ribosomal rpsL gene containing codon 43. EpSmR has a point mutation that altered this codon from lysine (AAA) to threonine (ACA). The strA and strB genes were not identified in EpSmR. EpSmR showed a high resistance to streptomycin (>50,000 μg/ml). This is the first study reporting EpSmR, which emerged due to a mutation in codon 43 of the rpsL gene.

Revealing Natural Intracellular Peptides in Gills of Seahorse Hippocampus reidi.

The seahorse is a marine teleost fish member of the Syngnathidae family that displays a complex variety of morphological and reproductive behavior innovations and has been recognized for its medicinal importance. In the Brazilian ichthyofauna, the seahorse Hippocampus reidi is among the three fish species most used by the population in traditional medicine. In this study, a protocol was performed based on fast heat inactivation of proteases plus liquid chromatography coupled to mass spectrometry to identify native peptides in gills of seahorse H. reidi. The MS/MS spectra obtained from gills allowed the identification of 1080 peptides, of which 1013 peptides were present in all samples and 67 peptide sequences were identified in an additional LC-MS/MS run from an alkylated and reduced pool of samples. The majority of peptides were fragments of the internal region of the amino acid sequence of the precursor proteins (67%), and N- and C-terminal represented 18% and 15%, respectively. Many peptide sequences presented ribosomal proteins, histones and hemoglobin as precursor proteins. In addition, peptide fragments from moronecidin-like protein, described with antimicrobial activity, were found in all gill samples of H. reidi. The identified sequences may reveal new bioactive peptides.

Imprints of α clustering in the density profiles of C12 and O16

The $^{4}$He nucleus is a well bound and highly correlated four-nucleon system that is also found in form of $\alpha$-clusters as substructure in nuclear many-body systems. The standard single-particle shell model cannot represent these four-body correlations. It is highly desirable to find a simple way to identify and distinguish these fundamental structures without large-scale computations. In this paper, we investigate with intrinsic Slater determinants as trial states in how far these two competing pictures prevail in the ground states of $^{12}$C and $^{16}$O. The trial states can describe both the $j$-$j$ coupling shell-model and $\alpha$-cluster configurations in a unified way. One-body density distributions of the trial states are calculated and compared to elastic scattering cross section data. The parameters of the trial state are chosen to reproduce the experimental charge radii. A well developed cluster structure is characterized by an enhancement of the differential elastic scattering cross sections, as well as the elastic charge form factors around the first peak positions. The density profiles of the internal regions can also be probed at higher momentum transfer regions beyond the second minimum. With these trial states one can visualize the competition between cluster and shell structure in an intuitive and simple way.

Dynamic interplay between non-coding enhancer transcription and gene activity in development

Non-coding transcription at the intergenic regulatory regions is a prevalent feature of metazoan genomes, but its biological function remains uncertain. Here, we devise a live-imaging system that permits simultaneous visualization of gene activity along with intergenic non-coding transcription at single-cell resolution in Drosophila. Quantitative image analysis reveals that elongation of RNA polymerase II across the internal core region of enhancers leads to suppression of transcriptional bursting from linked genes. Super-resolution imaging and genome-editing analysis further demonstrate that enhancer transcription antagonizes molecular crowding of transcription factors, thereby interrupting the formation of a transcription hub at the gene locus. We also show that a certain class of developmental enhancers are structurally optimized to co-activate gene transcription together with non-coding transcription effectively. We suggest that enhancer function is flexibly tunable through the modulation of hub formation via surrounding non-coding transcription during development.

Subsurface fatigue crack tip strains in 7475‐T7351 aluminium alloy measured using stroboscopic neutron diffraction

AbstractFatigue crack growth in thick‐section metals is typically controlled by an internal plane strain region where strong triaxial constraint of the crack tip occurs. However, the crack tip stress state in this region is challenging to measure. We have used neutron diffraction to study the plane strain section of fatigue crack tips in situ. A stroboscopic form of neutron diffraction using a moving frame‐of‐reference was developed to measure crack tip strains as a function of phase in the fatigue loading cycle without interrupting the cyclic load. Using point measurements of near‐tip strain in 7475‐T7351 aluminium alloy in conjunction with finite element analysis, we can estimate the extent of the crack tip plastic zone, verifying that it is small for this material and set of loading conditions.

On the Exponential Decay of Strongly Interacting Cold Atoms from a Double-Well Potential

In this article, we study an exponential decay for the gas of bosons with strong repulsive delta interactions from a double-well potential. We consider an exactly solvable model comprising an infinite wall and two Dirac delta barriers. We explore its features both within the exact method and with the resonance expansion approach. The study reveals the effect of the splitting barrier on the decay rate in dependence on the number of particles. Among other things, we find that the effect of the splitting barrier on the decay rate is most pronounced in systems with odd particle numbers. During exponential decay, the spatial correlations in an internal region are well captured by the “radiating state”.

Cis-Acting Element at the 5' Noncoding Region of Tacaribe Virus S RNA Modulates Genome Replication.

Tacaribe virus (TCRV) is the prototype of New World mammarenaviruses, a group that includes several members that cause hemorrhagic fevers in humans. The TCRV genome comprises two RNA segments, named S (small) and L (large). Both genomic segments contain noncoding regions (NCRs) at their 5' and 3' ends. While the 5'- and 3'-terminal 19-nucleotide sequences are known to be essential for promoter function, the role of their neighboring internal noncoding region (iNCR) sequences remains poorly understood. To analyze the relevance of the 5' and 3' iNCRs in TCRV S RNA synthesis, mutant S-like minigenomes and miniantigenomes were generated. Using a minireplicon assay, Northern blotting, and reverse transcription-quantitative PCR, we demonstrated that the genomic 5' iNCR is specifically engaged in minigenome replication yet is not directly involved in minigenome transcription, and we showed that the S genome 3' iNCR is barely engaged in this process. Analysis of partial deletions and point mutations, as well as total or partial substitution of the 5' iNCR sequence, led us to conclude that the integrity of the whole genomic 5' iNCR is essential and that a local predicted secondary structure or RNA-RNA interactions between the 5' and 3' iNCRs are not strictly required for viral S RNA synthesis. Furthermore, we employed a TCRV reverse genetic approach to ask whether manipulation of the S genomic 5' iNCR sequence may be suitable for viral attenuation. We found that mutagenesis of the 5' promoter-proximal subregion slightly impacted recombinant TCRV virulence in vivo. IMPORTANCE The Mammarenavirus genus of the Arenaviridae family includes several members that cause severe hemorrhagic fevers associated with high morbidity and mortality rates, for which no FDA-approved vaccines and limited therapeutic resources are available. We provide evidence demonstrating the specific involvement of the TCRV S 5' noncoding sequence adjacent to the viral promoter in replication. In addition, we examined the relevance of this region in the context of an in vivo infection. Our findings provide insight into the mechanism through which this 5' viral RNA noncoding region assists the L polymerase for efficient viral S RNA synthesis. Also, these findings expand our understanding of the effect of genetic manipulation of New World mammarenavirus sequences aimed at the rational design of attenuated recombinant virus vaccine platforms.

Spatial Heterogeneity in the Nonlinear Impact of Built Environment on Commuting Time of Active Users: A Gradient Boosting Regression Tree Approach

Many studies provided evidence regarding the influence of built environment (BE) on commuting time. However, few studies have considered the spatial heterogeneity of such impacts. Using data from Nanjing, China, this study employs two-step clustering and gradient boosted regression trees (GBRT) to segment the neighborhoods into different types and investigate the effects of BE characteristics on the commuting time of active users. The results show a strong effect of BE characteristics on commuting time, involving active modes. The importance of BE characteristics varies among neighborhood types. For active commuters in the internal region of Nanjing, commuting time is affected mostly by the land use mix at the work end. The lowest impact of BE in internal regions is associated with metro station density. For active commuters in external region of the city, the relative importance of intersection density at the home end is the largest (as high as 5.76%). Moreover, other significant differences are found in the associations between BE characteristics and active commuting time in the two regions.

Mobility of mPing and its associated elements is regulated by both internal and terminal sequences

BackgroundDNA transposable elements are mobilized by a “cut and paste” mechanism catalyzed by the binding of one or more transposase proteins to terminal inverted repeats (TIRs) to form a transpositional complex. Study of the rice genome indicates that the mPing element has experienced a recent burst in transposition compared to the closely related Ping and Pong elements. A previously developed yeast transposition assay allowed us to probe the role of both internal and terminal sequences in the mobilization of these elements.ResultsWe observed that mPing and a synthetic mPong element have significantly higher transposition efficiency than the related autonomous Ping and Pong elements. Systematic mutation of the internal sequences of both mPing and mPong identified multiple regions that promote or inhibit transposition. Simultaneous alteration of single bases on both mPing TIRs resulted in a significant reduction in transposition frequency, indicating that each base plays a role in efficient transposase binding. Testing chimeric mPing and mPong elements verified the important role of both the TIRs and internal regulatory regions. Previous experiments showed that the G at position 16, adjacent to the 5′ TIR, allows mPing to have higher mobility. Alteration of the 16th and 17th base from mPing’s 3′ end or replacement of the 3′ end with Pong 3′ sequences significantly increased transposition frequency.ConclusionsAs the transposase proteins were consistent throughout this study, we conclude that the observed transposition differences are due to the element sequences. The presence of sub-optimal internal regions and TIR bases supports a model in which transposable elements self-limit their activity to prevent host damage and detection by host regulatory mechanisms. Knowing the role of the TIRs, adjacent sub-TIRs, and internal regulatory sequences allows for the creation of hyperactive elements.

Apolipoprotein B in the Rough Endoplasmic Reticulum: Translation, Translocation and the Initiation of Lipoprotein Assembly

Apolipoprotein (apo) B and the microsomal triglyceride transfer protein are essential for the hepatic assembly and secretion of triglyceride-rich VLDL. To understand how apoB initiates the process of lipoprotein formation, interest has focused on the biogenesis of its amino terminal globular domain (α1 domain). When only this domain is expressed in hepatoma cells, no lipoprotein particle will form. However, proper folding of the α1 domain is essential for the internal lipophilic regions of apoB to engage in cotranslational lipid recruitment. The essential function of this domain may be related to its capacity to promote a specific physical interaction with the microsomal triglyceride transfer protein, necessary for apoB's proper folding and lipidation. Alternatively, this domain may promote an autonomous lipid recruitment step that nucleates microsomal triglyceride transfer protein-dependent lipid sequestration by apoB. Forms of apoB that fail to initiate particle assembly or forms associated with aberrant underlipidated particles are targeted for intracellular turnover. Two sites of apoB degradation have been identified. In hepatocarcinoma-derived cells, misassembled apoB may undergo progressive reverse translocation from the endoplasmic reticulum lumen to the cytosol, a process that is mechanistically coupled to polyubiquitination and proteasome-mediated degradation on the cytosolic side of the membrane. Alternatively, studies in primary hepatocytes reveal that apoB may undergo sorting to a post-endoplasmic reticulum compartment for presecretory degradation. In either case, the balance between assembly and presecretory degradation of apoB may represent a control point for the production of hepatic VLDL.

Study of decoupled gravastars in energy–momentum squared gravity

In this paper, we generate an exact anisotropic gravastar model using gravitational decoupling technique through minimal geometric deformation in the framework of f(ℜ,T2) gravity. This novel model explains an ultra-compact stellar configuration whose internal region is smoothly matched to the exterior region. The developed stellar model satisfies some of the essential characteristics of a physically acceptable model such as a positive monotonically decreasing profile of energy density from the center to the boundary and monotonically decreasing behavior of the pressure. The anisotropic factor and Schwarzschild spacetime follows physically acceptable behavior. We find that all the energy bounds are satisfied except strong energy condition inside the ultra-compact stellar structure for the coupling constant of this theory, which is compatible with the regularity condition.

Antimicrobial Resistance, SCCmec, Virulence and Genotypes of MRSA in Southern China for 7 Years: Filling the Gap of Molecular Epidemiology.

As the prevalence of Staphylococcus aureus infections is of worldwide concern, phenotype and genotype in prevalent MRSA strains require longitudinal investigation. In this study, the antibiotic resistance, virulence gene acquisition, and molecular type were determined on a large scale of nosocomial S. aureus strains in Southern China during 2009-2015. Bacterial identification and antimicrobial susceptibility to 10 antibiotics were tested by Vitek-2. Virulence genes encoding staphylococcal enterotoxins (SEA, SEB, SEC, SED, and SEE), exfoliative toxins (ETA and ETB), Panton-Valentine leukocidin (PVL), and toxic shock syndrome toxin (TSST) were detected by PCR, with SCCmec typing also conducted by multiplex PCR strategy. Genotypes were discriminated by MLST and spaA typing. MLST was performed by amplification of the internal region of seven housekeeping genes. PCR amplification targeting the spa gene was performed for spa typing. No resistance to vancomycin, linezolid, or quinupristin and increase in the resistance to trimethoprim/sulfamethoxazole (55.5%) were identified. A total of nine SCCmec types and subtypes, thirteen STs clustered into thirteen spa types were identified, with ST239-SCCmec III-t037 presenting the predominant methicillin-resistant S. aureus (MRSA) clone. Typically, SCCmec type IX and ST546 were emergent types in China. Isolates positive for both pvl and tsst genes and for both eta and etb genes were also identified. Important findings in this study include: firstly, we have provided comprehensive knowledge on the molecular epidemiology of MRSA in Southern China which fills the gap since 2006 or 2010 from previous studies. Secondly, we have presented the correlation between virulence factors (four major groups) and genotypes (SCCmec, ST and spa types). Thirdly, we have shown evidence for earliest emergence of type I SCCmec from 2012, type VI from 2009 and type XI from 2012 in MRSA from Southern China.

Catalytic Pt/Al2O3 Monolithic Foam for Ethanol Reforming Fabricated by the Competitive Impregnation Method.

Here, the synthesis of Pt/Al2O3 catalysts on a monolithic foam employing the competitive impregnation method is presented. NO3 - was used as a competitive adsorbate at different concentrations in order to delay the adsorption of Pt, minimizing the formation of Pt concentration gradients throughout the monolith. The catalysts' characterization includes the BET, H2-pulse titration, SEM, XRD and XPS techniques. The catalytic activity evaluation was performed under partial oxidation and autothermal reforming of ethanol in a short contact time reactor. The competitive impregnation method was able to produce better dispersion of the Pt particles through the Al2O3 foams. XPS analysis indicated the catalytic activity of the samples, by the presence of metallic Pt and Pt oxides (PtO and PtO2) in the internal regions of the monoliths. Compared to other Pt catalysts reported in the literature, the catalyst produced by the competitive impregnation method was revealed to be selective toward H2. Overall, the results showed that the competitive impregnation method employing NO3 - as the co-adsorbate is a promising technique to synthesize well dispersed Pt catalysts over α-Al2O3 foams.

Study on Performance Simulation of Vascular-like Flow Channel Model Based on TPMS Structure

In medical validation experiments, such as drug testing and clinical trials, 3D bioprinted biomimetic tissues, especially those containing blood vessels, can be used to replace animal models. The difficulty in the viability of printed biomimetic tissues, in general, lies in the provision of adequate oxygen and nutrients to the internal regions. This is to ensure normal cellular metabolic activity. The construction of a flow channel network in the tissue is an effective way to address this challenge by both allowing nutrients to diffuse and providing sufficient nutrients for internal cell growth and by removing metabolic waste in a timely manner. In this paper, a three-dimensional TPMS vascular flow channel network model was developed and simulated to analyse the effect of perfusion pressure on blood flow rate and vascular-like flow channel wall pressure when the perfusion pressure varies. Based on the simulation results, the in vitro perfusion culture parameters were optimised to improve the structure of the porous structure model of the vascular-like flow channel, avoiding perfusion failure due to unreasonable perfusion pressure settings or necrosis of cells without sufficient nutrients due to the lack of fluid passing through some of the channels, and the research work promotes the development of tissue engineering in vitro culture.

Geography of science: Competitiveness and inequality

Using ideas and tools of complexity science we design a holistic measure of \textit{Scientific Fitness}, encompassing the scientific knowledge, capabilities and competitiveness of a research system. We characterize the temporal dynamics of Scientific Fitness and R\&D expenditures at the geographical scale of nations, highlighting patterns of similar research systems, and showing how developing nations (China in particular) are quickly catching up the developed ones. Down-scaling the aggregation level of the analysis, we find that even developed nations show a considerable level of inequality in the Scientific Fitness of their internal regions. Further, we assess comparatively how the competitiveness of each geographic region is distributed over the spectrum of research sectors. Overall, the Scientific Fitness represents the first high quality estimation of the scientific strength of nations and regions, opening new policy-making applications for better allocating resources, filling inequality gaps and ultimately promoting innovation.

An analytical solution of the effectiveness factor of photocatalytic reactors based on Robin boundary conditions

An analytical expression of the effectiveness factor of photocatalytic reactors that accounts for external mass transfer limitations is presented. The solution is based on Robin boundary conditions introducing the Sherwood number as the parameter that accounts for the external mass transfer limitations. Regions highlighting free diffusion, diffusion limitations, and external mass transfer limitations are identified based on the Thiele Modulus and the Sherwood number. At low values of the Sherwood number, the internal diffusion and reaction rate-limiting regions are surpassed by the external mass transfer limitations. A cut-off value of the Sherwood number below which external mass transfer limitations cannot be ignored is 0.55. The evaluation of the model showed that under Dirichlet boundary condition the model converges to literature models from similar studies. This 1-D model looked at the Sherwood number across a broad scope and accounted for a broader range of limitations associated with immobilized photocatalytic films.

Uncovering the molecular grammar of IDPs in desiccation tolerance.

Tardigrades, aka water bears, are remarkable for their ability to survive many environmental stresses, including desiccation (extreme drying). Desiccation tolerance in tardigrades depends on the accumulation of several families of intrinsically disordered proteins (IDPs), of which Cytosolic Abundant Heat Soluble (CAHS) proteins are essential to survive desiccation. Beyond tardigrades, CAHS proteins can also improve desiccation tolerance in heterologous systems and prevent desiccation-induced protein damage in vitro. However, what sequence features drive CAHS protein function is unknown. Understanding the CAHS sequence-ensemble-function relationship will shed light on the molecular mechanisms by which tardigrades survive extreme stresses. Using a model CAHS protein, CAHS D, we show that helix formation is important for its protective capacity. Utilizing a rational mutagenesis approach, we find that an internal linker region is the protective portion of CAHS D. We find that within this linker region specific sequence features such as charge identity, hydrophobicity, and amino acid organization dictate specific biophysical properties, such as helix formation, and are correlated to the desiccation protection in vitro. However, small helical peptides by themselves cannot confer the same levels of protection as CAHS D. This indicates that along with helicity, other features likely play a role in determining the protective capacity of CAHS D. These findings support the existing theory of helicity provided protection by different stress-tolerant LEA proteins. Understanding CAHS D's sequence-structure-function relationship will not only provide insights into how IDP sequences dictate their conformational dynamics and functional properties, but can also be useful for real-world applications like designing stress-tolerant crops or helping increase the shelf-life of sensitive biomedical materials in a dry state.