Large Complex Research Articles

DrugDomain: The evolutionary context of drugs and small molecules bound to domains.

Interactions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signaling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity. Therefore, many drugs available on the market today are small molecules (72% of all approved drugs in the last 5 years). Proteins are composed of one or more domains: evolutionary units that convey function or fitness either singly or in concert with others. Understanding which domain(s) of the target protein binds to a drug can lead to additional opportunities for discovering novel targets. The evolutionary classification of protein domains (ECOD) classifies domains into an evolutionary hierarchy that focuses on distant homology. Previously, no structure-based protein domain classification existed that included information about both the interaction between small molecules or drugs and the structural domains of a target protein. This data is especially important for multidomain proteins and large complexes. Here, we present the DrugDomain database that reports the interaction between ECOD of human target proteins and DrugBank molecules and drugs. The pilot version of DrugDomain describes the interaction of 5160 DrugBank molecules associated with 2573 human proteins. It describes domains for all experimentally determined structures of these proteins and incorporates AlphaFold models when such structures are unavailable. The DrugDomain database is available online: http://prodata.swmed.edu/DrugDomain/.

A single-domain antibody library based on a stability-engineered human VH3 scaffold

Using conventional immunoglobulin G (IgG) molecules as therapeutic agents presents several well-known disadvantages owing to their large size and structural complexity, negatively impacting development and production efficiency. Single-domain antibodies (sdAbs) are the smallest functional antibody format (~ 15 kDa) and represent a viable alternative to IgG in many applications. However, unlike natural single-domain antibodies, such as camelid VHH, the variable domains of conventional antibodies show poor physicochemical properties when expressed as sdAbs. This report identified stable sdAb variants of human VH3-23 from a framework region 2-randomized human VH library by phage display selection under thermal challenge. Synthetic complementarity determining region diversity was introduced to one of the selected variants with high thermal stability, expression level, and monomeric content to construct a human VH sdAb library. The library was validated by panning against a panel of antigens, and target-specific binders were identified and characterized for their affinity and biophysical properties. The results of this study suggest that a synthetic sdAb library based on a stability-engineered human VH scaffold could be a facile source of high-quality sdAb for many practical applications.

“Architecture, construction system and functioning of the roman saltworks of O Areal (Vigo-Galicia-Spain). A reference in the investigation of salt production in the roman world”

These Roman saltworks are located in the city of Vigo, in the northwest of the Iberian Peninsula, and they were part of a large industrial complex, dedicated to the production of sauces and salted fish. To this day, they are the best-preserved solar evaporation marine saltworks evidences in the Roman world, making it possible to know the entire production cycleBased on ceramic contexts and C14 data, we have concluded a period of use around the 1st-3rd c. AD, which falls completely within what is known as the Warm Roman Period.The architecture of the salt complex is articulated through different types of ponds, of various dimensions and construction characteristics. They use different materials for their construction: stone, ceramics, silt, clay, wood or sand. Its characteristics and dimensions are in accordance with its function within the salt production cycle: decanters, evaporators and crystallizers. Other architectural elements complete the ensemble and help to understand its functioning in detail.Knowledge of the architecture, constructive techniques and morphology of these saltworks has made it possible to identify others even when excavated on small surfaces, thanks to the archaeological indicators that the study of these salt pans allows us to define.

Functionality of the V-type ATPase during asexual growth and development of Plasmodium falciparum

V-type ATPases are highly conserved hetero-multi-subunit proton pumping machineries found in all eukaryotes. They utilize ATP hydrolysis to pump protons, acidifying intracellular or extracellular compartments, and are thus crucial for various biological processes. Despite their evolutionary conservation in malaria parasites, this proton pump remains understudied. To understand the localization and biological functions of Plasmodium falciparum V-type ATPase, we employed CRISPR/Cas9 to endogenously tag the subunit A of the V1 domain. V1A (PF3D7_1311900) was tagged with a triple hemagglutinin epitope and the TetR-DOZI-aptamer system for conditional expression under the regulation of anhydrotetracycline. Via immunofluorescence assays, we identified that V-type ATPase is expressed throughout the intraerythrocytic developmental cycle and is mainly localized on the digestive vacuole and parasite plasma membrane. Immuno-electron microscopy further revealed that V-type ATPase is also localized on secretory organelles in merozoites. Knockdown of V1A led to cytosolic pH imbalance and blockage of hemoglobin digestion in the digestive vacuole, resulting in an arrest of parasite development in the trophozoite stage and, ultimately, parasite demise. Using Bafilomycin A1, a specific inhibitor of V-type ATPases, we found that the P. falciparum V-type ATPase is likely involved in parasite invasion but is not critical for ring stage development. Further, we detected a large molecular weight complex in BN-PAGE (∼ 1.0 MDa), corresponding to the total molecular weights of V1 and Vo domains. Together, we show that V-type ATPase is localized on multiple subcellular compartments in P. falciparum, and its functionality throughout the asexual cycle varies depending on the parasite developmental stages.

Preparation of Dendrobium officinale Polysaccharide by Lactic Acid Bacterium Fermentation and Its Protective Mechanism against Alcoholic Liver Damage in Mice.

Dendrobium officinale polysaccharide (DP) was prepared with lactic acid bacterium fermentation to overcome the large molecular weight and complex structure of traditional DP for improving its functional activity and application range in this work. The structure was analyzed, and then the functional activity was evaluated using a mouse model of alcoholic liver damage. The monosaccharide compositions were composed of four monosaccharides: arabinose (0.13%), galactose (0.50%), glucose (24.38%), and mannose (74.98%) with a molecular weight of 2.13 kDa. The connection types of glycosidic bonds in fermented D. officinale (KFDP) were →4)-β-D-Manp(1→, →4)-β-Glcp(1→, β-D-Manp(1→, and β-D-Glcp(1→. KFDP exhibited an excellent protective effect on alcoholic-induced liver damage at a dose of 80 mg/kg compared with polysaccharide separated and purified from D. officinale without fermentation (KDP), which increased the activity of GSH, GSH-Px, and GR and decreased the content of MDA, AST, T-AOC, and ALT, as well as regulated the level of IL-6, TNF-α, and IL-1β to maintain the normal functional structure of hepatocytes and retard the apoptosis rate of hepatocytes. The results proved that fermentation degradation is beneficial to improving the biological activity of polysaccharides. The potential mechanism of KFDP in protecting alcoholic liver damage was inhibiting the expression of miRNA-150-5p and targeting to promote the expression of Pik3r1. This study provides an important basis for the development of functional foods.

Hyperspectral Image Analysis Using Cloud-Based Support Vector Machines

Hyperspectral image processing techniques involve time-consuming calculations due to the large volume and complexity of the data. Indeed, hyperspectral scenes contain a wealth of spatial and spectral information thanks to the hundreds of narrow and continuous bands collected across the electromagnetic spectrum. Predictive models, particularly supervised machine learning classifiers, take advantage of this information to predict the pixel categories of images through a training set of real observations. Most notably, the Support Vector Machine (SVM) has demonstrate impressive accuracy results for image classification. Notwithstanding the performance offered by SVMs, dealing with such a large volume of data is computationally challenging. In this paper, a scalable and high-performance cloud-based approach for distributed training of SVM is proposed. The proposal address the overwhelming amount of remote sensing (RS) data information through a parallel training allocation. The implementation is performed over a memory-efficient Apache Spark distributed environment. Experiments are performed on a benchmark of real hyperspectral scenes to show the robustness of the proposal. Obtained results demonstrate efficient classification whilst optimising data processing in terms of training times.

Oocyte-specific EXOC5 expression is required for mouse oogenesis and folliculogenesis.

EXOC5 is a crucial component of a large multi-subunit tethering complex, the exocyst complex, that is required for fusion of secretory vesicles with the plasma membrane. Exoc5 deleted mice die as early embryos. Therefore, to determine the role of EXOC5 in follicular and oocyte development, it was necessary to produce a conditional knockout (cKO), Zp3-Exoc5-CKO, in which Exoc5 was deleted only in oocytes. The first wave of folliculogenesis appeared histologically normal and progressed to the antral stage. However, after in vitro fertilization with normal sperm, oocytes collected from the first wave (superovulated 21-day old cKO mice) were shown to be developmentally incompetent. Adult follicular waves did not progress beyond the secondary follicle stage where they underwent apoptosis. Female cKO mice were infertile. Overall, these data suggest that the first wave of folliculogenesis is less sensitive to oocyte-specific loss of Exoc5, but the resulting gametes have reduced developmental competence. In contrast, subsequent waves of folliculogenesis require oocyte-specific Exoc5 for development past the preantral follicle stage. The Zp3-Exoc5-CKO mouse provides a model for disrupting folliculogenesis that also enables the separation between the first and subsequent waves of folliculogenesis.

The roman saltworks of the Atlantic coast of Gallaecia: Traces and evidence of a large sea salt production complex

Judging by the numerous references to its many uses and applications in the literary sources, salt was a precious commodity in Antiquity. However, the archaeological traces of sea salt production are rather scarce with only a few known sites throughout the Mediterranean preserving remains of ancient salinae. In the Roman Empire as a whole, it is the northwest of the Iberian Peninsula that has provided the greatest amount of direct evidence of sea salt production. After analysing the archaeological evidence documented in excavations and field surveys conducted during the past 10 years, this paper describes the Roman salt landscapes on the Atlantic coast of ancient Gallaecia, the distribution of evidence, and the chronological indicators allowing to date them to the Roman Imperial period. The legal and tax system determining the forms of ownership and labour organization of saltworks is also examined. In light of the results, it is possible to conclude that on the northwest Atlantic coast of the Iberian Peninsula there was a major sea salt and fish salting production network which had a direct impact on the socioeconomic structure of provincial society.

Genetic diversity of Plasmodium malariae in sub-Saharan Africa: a two-marker genotyping approach for molecular epidemiological studies

IntroductionPlasmodium malariae is the most common non-falciparum species in sub-Saharan Africa. Despite this, data on its genetic diversity is scarce. Therefore, we aimed to establish a P. malariae genotyping approach based on size polymorphic regions that can be easily applied in molecular epidemiological studies.MethodsFour potential genotyping markers, Pm02, Pm09, P. malariae thrombospondin-related anonymous protein (pmtrap), and P. malariae merozoite surface protein fragment 2 (pmmsp1 F2) were amplified via nested PCR and analysed using automated capillary gel electrophoresis.ResultsWe observed the highest allelic diversity for pmtrap (MOI = 1.61) and pmmsp1 F2 (He = 0.81). Further applying the two markers pmtrap and pmmsp1 F2 on a different sample set of 21 P. malariae positive individuals followed up over one week, we saw a high consistency in their performance. The results show a large complexity and high dynamics of P. malariae infections in the asymptomatic Gabonese study population.DiscussionWe successfully implemented a new genotyping panel for P. malariae consisting of only two markers: pmtrap and pmmsp1 F2. It can be easily applied in other settings to investigate the genotype diversity of P. malariae populations, providing further important data on the molecular epidemiology of this parasite species.

Dendritically localized RNAs are packaged as diversely composed Ribonucleoprotein particles with heterogeneous copy number states.

Localization of mRNAs to dendrites is a fundamental mechanism by which neurons achieve spatiotemporal control of gene expression. Translationally repressed neuronal mRNA transport granules, also referred to as ribonuclear proteins (RNPs), have been shown to be trafficked as single or low copy number RNPs and as larger complexes with multiple copies and/or species of mRNAs. However, there is little evidence of either population in intact neuronal circuits. Using single molecule fluorescence in situ hybridization studies in the dendrites of adult rat and mouse hippocampus, we provide evidence that supports the existence of multi-transcript RNPs with the constituents varying in amounts for each RNA species. By competing-off fluorescently labeled probe with serial increases of unlabeled probe, we detected stepwise decreases in Arc RNP number and fluorescence intensity, suggesting Arc RNAs localize to dendrites in both low- and multiple-copy number RNPs. When probing for multiple mRNAs, we find that localized RNPs are heterogeneous in size and colocalization patterns that vary per RNA. Further, localized RNAs that are targeted by the same trans-acting element (FMRP) display greater levels of colocalization compared to an RNA not targeted by FMRP. Simultaneous visualization and assessment of colocalization using highly multiplexed imaging of a dozen mRNA species targeted by FMRP demonstrates that dendritic RNAs are mostly trafficked as heteromeric cargoes of multiple types of RNAs (at least one or more RNAs). Moreover, the composition of these RNA cargoes correlates with the abundance of the transcripts even after accounting for expression. Collectively, these results suggest that dendritic RNPs are packaged as heterogeneous co-assemblies of different mRNAs and that RNP contents may be driven, at least partially, by highly abundant dendritic RNAs; a model that favors efficiency over fine-tuned control for sustaining long-distance trafficking of thousands of messenger molecules.

Beyond large complex structure: quantized periods and boundary data for one-modulus singularities

We study periods in an integral basis near all possible singularities in one-dimensional complex structure moduli spaces of Calabi-Yau threefolds. Near large complex structure points these asymptotic periods are well understood in terms of the topological data of the mirror Calabi-Yau manifold. The aim of this work is to characterize the period data near other boundaries in moduli space such as conifold and K-points. Using results from Hodge theory, we provide the general form of these periods in a quantized three-cycle basis. Based on these periods we compute the prepotential and related physical couplings of the underlying supergravity theory. Moreover, we elucidate the meaning of the model-dependent coefficients that appear in these expressions: these can be identified with certain topological and arithmetic numbers associated to the singular geometry at the moduli space boundary. We illustrate our findings by studying a wide set of examples.

Chip-scale integrated holographic devices based on top-emitting vertical cavity surface emitting lasers.

Holography technology is considered the ultimate three-dimensional (3D) visualization technology in the future. However, conventional methods for achieving holography generally utilize discrete optical components and off-chip laser sources, resulting in a large size and high complexity, which are undesirable for practical applications. In this Letter, chip-scale integrated holographic devices are realized by integrating top-emitting vertical cavity surface emitting lasers (VCSELs) with micro holograms printed by 3D femtosecond laser nanoprinting technology. The VCSELs are designed to operate in a single fundamental mode with a Gaussian emission profile. Then the Gaussian beams are phase-modulated by the integrated micro holograms designed by the Gerchberg-Saxton (GS) algorithm and the target holographic images can be displayed behind the holograms. Such integrated holographic devices are of micron size and can be easily scaled into arrays with arbitrary channels on-demand, which are important for achieving miniaturized and portable holographic imaging systems.

Ultraviolet color image sensor based on CsPbBr3 inorganic perovskite nanocrystal film.

Ultraviolet and color imaging require different image sensors and optical channels, which results in large size, complex structure, and high cost of imaging systems. Here, we report a novel, to the best of our knowledge, image sensor that combines ultraviolet and color imaging functions. The fabrication of this image sensor is achieved by coating high-transparency CsPbBr3 perovskite nanocrystals in a polymer film on the color filter layer of a silicon-based detector. The film, serving as an ultraviolet photoluminescent layer, exhibits high transparency, exceeding 91.5% at wavelengths beyond the photoluminescence peak of 513 nm. During ultraviolet imaging, the film converts ultraviolet light into visible light, which passes through the green filter layer to reach the detector for imaging. During visible light imaging, red light, green light, and most of the blue light pass through the CsPbBr3 perovskite nanocrystal film and color filter layer to reach the detector for imaging. As a result, the image sensor can capture both 257 nm solar-blind ultraviolet images and color photos in the visible light.

Comparative immunohematological profile of <i>Pelophylax ridibundus</i> and <i>P. lessonae</i> (Amphibia: Ranidae) infected with hemoparasites

The direction of adaptive reactions of healthy and Hepatozoon spp.-infected green frogs from water bodies of the Nizhni Novgorod region with various hydrochemical conditions was studied. During the observation period, infection of pool frogs and an increase in the total population indicators of infection of male and female marsh frogs with Hepatozoon spp. were revealed. Hypertrophy of the morphometric parameters of infected blood erythrocytes compared with healthy cells was revealed in marsh frogs. The content of neutrophil granulocytes in the blood of infected marsh frogs was higher compared to healthy individuals, while the level of immune complexes did not differ. In infected pool frogs, an increase in the level of large immune complexes in the blood serum and the enlargement index was revealed compared to healthy ones against the background of a general decrease in the body’s resistance in conditions of severe pollution of their habitat with heavy metals and sulfates. For marsh frogs, a correlation was established between the proportion of infected erythrocytes and the content of myelocytes and young forms of neutrophils in the blood; while for pool frogs – with the content of neutrophils and the enlargement index of immune complexes. The method of multifactorial dispersion analysis revealed a significant influence of such factors as gender and the interaction of gender/infection with hemoparasites on the immune status of amphibians.

Validation of AERMOD Prediction Accuracy for Particulate Matters (PM10, PM2.5) for a Large Coal Mine Complex: A Multisource Perspective

Validation of AERMOD Prediction Accuracy for Particulate Matters (PM10, PM2.5) for a Large Coal Mine Complex: A Multisource Perspective

IDRWalker: A Random Walk Based Tool for Generating Intrinsically Disordered Regions in Large Protein Complexes.

Intrinsically disordered regions (IDRs), which may be functionally important, are common in proteins. However, the structures of IDRs are often missing due to their highly dynamic nature. In the study of IDRs, integrative modeling combining computational simulations and experimental data is a common approach, for which initial structures of the IDRs need to be built. However, applying this method to large protein complexes is challenging because existing structure generation tools are sometimes unsuitable for IDRs in large systems. To facilitate convenient and rapid structure generation of IDRs in large protein complexes, we developed a computational tool named IDRWalker based on self-avoiding random walks. Three protein complexes were used to illustrate the efficiency of the tool, and it was found that IDRs in more than 800 chains of the nuclear pore complex could be generated in minutes. These structures of large protein complexes with added IDRs can be further used to run computational simulations for integrative modeling.

An antibody that inhibits TGF-β1 release from latent extracellular matrix complexes attenuates the progression of renal fibrosis.

Inhibitors of the transforming growth factor-β (TGF-β) pathway are potentially promising antifibrotic therapies, but nonselective simultaneous inhibition of all three TGF-β homologs has safety liabilities. TGF-β1 is noncovalently bound to a latency-associated peptide that is, in turn, covalently bound to different presenting molecules within large latent complexes. The latent TGF-β-binding proteins (LTBPs) present TGF-β1 in the extracellular matrix, and TGF-β1 is presented on immune cells by two transmembrane proteins, glycoprotein A repetitions predominant (GARP) and leucine-rich repeat protein 33 (LRRC33). Here, we describe LTBP-49247, an antibody that selectively bound to and inhibited the activation of TGF-β1 presented by LTBPs but did not bind to TGF-β1 presented by GARP or LRRC33. Structural studies demonstrated that LTBP-49247 recognized an epitope on LTBP-presented TGF-β1 that is not accessible on GARP- or LRRC33-presented TGF-β1, explaining the antibody's selectivity for LTBP-complexed TGF-β1. In two rodent models of kidney fibrosis of different etiologies, LTBP-49247 attenuated fibrotic progression, indicating the central role of LTBP-presented TGF-β1 in renal fibrosis. In mice, LTBP-49247 did not have the toxic effects associated with less selective TGF-β inhibitors. These results establish the feasibility of selectively targeting LTBP-bound TGF-β1 as an approach for treating fibrosis.

An antibody that inhibits TGF-β1 release from latent extracellular matrix complexes attenuates the progression of renal fibrosis.

Inhibitors of the transforming growth factor-β (TGF-β) pathway are potentially promising antifibrotic therapies, but nonselective simultaneous inhibition of all three TGF-β homologs has safety liabilities. TGF-β1 is noncovalently bound to a latency-associated peptide that is, in turn, covalently bound to different presenting molecules within large latent complexes. The latent TGF-β-binding proteins (LTBPs) present TGF-β1 in the extracellular matrix, and TGF-β1 is presented on immune cells by two transmembrane proteins, glycoprotein A repetitions predominant (GARP) and leucine-rich repeat protein 33 (LRRC33). Here, we describe LTBP-49247, an antibody that selectively bound to and inhibited the activation of TGF-β1 presented by LTBPs but did not bind to TGF-β1 presented by GARP or LRRC33. Structural studies demonstrated that LTBP-49247 recognized an epitope on LTBP-presented TGF-β1 that is not accessible on GARP- or LRRC33-presented TGF-β1, explaining the antibody's selectivity for LTBP-complexed TGF-β1. In two rodent models of kidney fibrosis of different etiologies, LTBP-49247 attenuated fibrotic progression, indicating the central role of LTBP-presented TGF-β1 in renal fibrosis. In mice, LTBP-49247 did not have the toxic effects associated with less selective TGF-β inhibitors. These results establish the feasibility of selectively targeting LTBP-bound TGF-β1 as an approach for treating fibrosis.

RESC14 and RESC8 cooperate to mediate RESC function and dynamics during trypanosome RNA editing.

Mitochondrial transcripts in Trypanosoma brucei require extensive uridine insertion/deletion RNA editing to generate translatable open reading frames. The RNA editing substrate binding complex (RESC) serves as the scaffold that coordinates the protein-protein and protein-RNA interactions during editing. RESC broadly contains two modules termed the guide RNA binding complex (GRBC) and the RNA editing mediator complex (REMC), as well as organizer proteins. How the protein and RNA components of RESC dynamically interact to facilitate editing is not well understood. Here, we examine the roles of organizer proteins, RESC8 and RESC14, in facilitating RESC dynamics. High-throughput sequencing of editing intermediates reveals an overlapping RESC8 and RESC14 function during editing progression across multiple transcripts. Blue native PAGE analysis demonstrates that RESC14 is essential for incorporation of RESC8 into a large RNA-containing complex, while RESC8 is important in recruiting a smaller ribonucleoprotein complex (RNP) to this large complex. Proximity labeling shows that RESC14 is important for stable RESC protein-protein interactions, as well as RESC-RECC associations. Together, our data support a model in which RESC14 is necessary for assembly of editing competent RESC through recruitment of an RNP containing RESC8, GRBC and gRNA to REMC and mRNA.

RESC14 and RESC8 cooperate to mediate RESC function and dynamics during trypanosome RNA editing.

Mitochondrial transcripts in Trypanosoma brucei require extensive uridine insertion/deletion RNA editing to generate translatable open reading frames. The RNA editing substrate binding complex (RESC) serves as the scaffold that coordinates the protein-protein and protein-RNA interactions during editing. RESC broadly contains two modules termed the guide RNA binding complex (GRBC) and the RNA editing mediator complex (REMC), as well as organizer proteins. How the protein and RNA components of RESC dynamically interact to facilitate editing is not well understood. Here, we examine the roles of organizer proteins, RESC8 and RESC14, in facilitating RESC dynamics. High-throughput sequencing of editing intermediates reveals an overlapping RESC8 and RESC14 function during editing progression across multiple transcripts. Blue native PAGE analysis demonstrates that RESC14 is essential for incorporation of RESC8 into a large RNA-containing complex, while RESC8 is important in recruiting a smaller ribonucleoprotein complex (RNP) to this large complex. Proximity labeling shows that RESC14 is important for stable RESC protein-protein interactions, as well as RESC-RECC associations. Together, our data support a model in which RESC14 is necessary for assembly of editing competent RESC through recruitment of an RNP containing RESC8, GRBC and gRNA to REMC and mRNA.