Aggregated Form Research Articles

Fermentation, immobilization, and application of de-acylase for biosynthesis of anti-fungal intermediates

The enzymatic synthesis of antifungal intermediates is receiving huge attention due to global demand. A de-acylase (EC 3.5.1.98) was produced by recombinant Streptomyces lividans using minimal salt media under optimized conditions. The recombinant S. lividans was subjected to fermentation for 90 h followed by enzyme isolation by KCl extraction method. Further, it was concentrated by tangential flow filter (TFF). Produced de-acylase was immobilized in the form of cross-linked enzyme aggregates (CLEAs) to prepare a robust formulation for further applications. In order to make de-acylase CLEAs, de-acylase was precipitated by ammonium sulphate (100% saturation) and cross-linked by glutaraldehyde (0.5% v/v). The immobilized CLEAs were lyophilized, and was utilized for synthesizing micafungin precursor-2 (FR179642) from the micafungin precursor-1 (FR901379). It was found that the de-acylase CLEAs exhibited more than 96% molar yield which were more efficient than free enzyme (showed nearly 65% molar yield) after 12 h of reaction. In the end, the prepared CLEAs were effectively recycled for five cycles with the retention of 55% residual activity and stored for 24 days without observable loss of activity.

Fish SCD1 promotes SGIV infection via modulating the formation of lipid droplets and TBK1/MDA5-activated IFN signal pathway

Stearoyl CoA desaturase (SCD1), the rate-limiting enzyme for monounsaturated fatty acid production, involved in host metabolic regulation. Recent reports indicated that SCD1 played a crucial role in the process of viral infection. To investigate the function of SCD1 in teleost fish and the role it played in fish virus infection, EcSCD1 was cloned and characterized in the orange-spotted grouper, Epinephelus coioides. The open reading frame (ORF) of EcSCD1 consisted of 1005 nucleotides encoding a protein containing 334 amino acids with a predicted molecular weight of 38.33 kDa, which shared 74.05% and 60.48% identity with zebrafish and human, respectively. EcSCD1 possessed four transmembrane domains and three conserved His-rich regions. In healthy groupers, EcSCD1 was primarily expressed in the liver and brain. Subcellular localization assay revealed that EcSCD1 was mainly distributed in the cytoplasm with uniform distribution or dot-like aggregation forms, and EcSCD1 was co-localized with the endoplasmic reticulum (ER). Singapore grouper iridovirus (SGIV) as well as poly (dA: dT) stimulation induced the expression of EcSCD1. On the other hand, EcSCD1 overexpression increased SGIV infection and SCD1 enzymatic product oleic acid (OA) recovered SGIV infection suppressed by SCD1 inhibitor. In addition, EcSCD1 overexpression facilitated the formation of lipid droplets (LDs), which was crucial for SGIV replication. Furthermore, EcSCD1 overexpression down-regulated the expression of interferon signaling molecules and the activities of interferon (IFN)1/3 and interferon stimulated response element (ISRE) promotors. Moreover, EcSCD1 overexpression restricted TANK binding kinase 1 (TBK1)−/melanoma differentiation-associated protein 5 (MDA5)-, but not mitochondrial antiviral signaling protein (MAVS)-evoked interferon immune responses. Overall, our findings offered novel insights into the regulatory mechanism of EcSCD1 during virus infection.

Chiral Diketopyrrolo[3,4-c]pyrrole-1,2,3-1H-triazole Dyes with Highly Tuneable Properties in Solution and Thin Films.

Invited for the cover of this issue are the research groups of Lorenzo Di Bari at the University of Pisa and Gianluca Maria Farinola at the University of Bari Aldo Moro. The image depicts three diketopyrrolo[3,4-c]pyrrole-1,2,3-1H-triazole dyes with the same chiral appendage R* but different achiral substituent groups Y showing profoundly different features in their aggregated form. Read the full text of the article at 10.1002/chem.202300291.

Elemental Composition of Plankton Exometabolites (Mucous Macroaggregates): Control by Biogenic and Lithogenic Components.

Among the various exometabolitic effects of marine microorganisms, massive mucilage events in the coastal zones of temperate and tropical seas are the most spectacular and environmentally important. Abundant mucilage material in the form of aggregates appears in late spring/early summer in the water column of the Adriatic Sea. These macroaggregate biopolymers originate mainly from plankton exometabolites, with both autochthonous and allochthonous components, and strongly impact the tourism, fisheries, and economy of coastal countries. In contrast to extensive studies on the structural and chemical nature of macroaggregates performed over past decades, the full elemental composition of these substances remains poorly known, which does not allow for a complete understanding of their origin, evolution, and necessary remediation measures. Here, we report the results of comprehensive analyses of 55 major and trace elements in the composition of macro aggregates collected at the surface and in the water column during massive mucilage events. Through normalization of the elemental chemical composition of the upper earth crust (UCC), river suspended material (RSM), mean oceanic plankton, and mean oceanic particulate suspended material, we demonstrate that the water column macroaggregates reflect a superposition of the signal from plankton and marine particulate matter. The surface macroaggregates were preferentially enriched in lithogenic component, and carried the signature of planktonic material. The rare earth element (REE) signal was strongly dominated by plankton and, to a lesser degree, by oceanic particulate matter, while at the same time being strongly (>80 times) impoverished compared with UCC and RSM. Taken together, the elemental composition of macroaggregates allows for distinguishing the lithogenic and biogenic impacts on the occurrence of these unique large-scale mucilage events, linked to the exometabolism of marine plankton combined with the input of allochthonous inorganic material.

Antibody aggregation can lead to reduced Protein A binding capacity and low step yield

Protein A affinity chromatography has been widely used for antibody capture and initial purification. In general, the yield of this step is relatively high (i.e., >90%). However, recently while purifying a bispecific antibody (bsAb) in appended IgG format, the Protein A capture step experienced low yield (i.e., ∼80%). It was found that the target bsAb started appearing in flow-through at a relatively low load density, suggesting that a portion of the expressed bsAb has compromised Protein A binding capability. Further studies indicated that the bsAb in flow-through was mainly in aggregate form. In addition, normal Protein A step yield was restored when the column was loaded with bsAb monomer. Thus, all the evidence pointed to the fact that aggregate with compromised binding capacity was the cause of low Protein A step yield in this case.

Heme-Aβ in SDS micellar environment: Active site environment and reactivity

Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disorder that causes brain cell death. Oxidative stress derived from the accumulation of redox cofactors like heme in amyloid plaques originating from amyloid β (Aβ) peptides has been implicated in the pathogenesis of AD. In the past our group has studied the interactions and reactivities of heme with soluble oligomeric and aggregated forms of Aβ. In this manuscript we report the interaction of heme with Aβ that remains membrane bound using membrane mimetic SDS (sodium dodecyl sulfate) micellar medium. Employing different spectroscopic techniques viz. circular dichroism (CD), absorption (UV–Vis), electron paramagnetic resonance (EPR) and resonance Raman (rR) we find that Aβ binds heme using one of its three His (preferentially His13) in SDS micellar medium. We also find that Arg5 is an essential distal residue responsible for higher peroxidase activity of heme bound Aβ in this membrane mimetic environment than free heme. This peroxidase activity exerted by even membrane bound heme-Aβ can potentially be more detrimental as the active site remains close to membranes and can hence oxidise the lipid bilayer of the neuronal cell, which can induce cell apoptosis. Thus, heme-Aβ in solution as well as in membrane-bound form are detrimental.

School entrance examinations as a small-scale data source for health monitoring of children using obesity as an example.

In the scope of the nationwide obligatory school entrance examinations (SEE), a standardised assessment of the preparedness for school of preschool children takes place in the federal states of Germany. For this purpose, height and weight of the children are determined. These data are available in aggregated form at county level, but are not yet being regularly compiled and processed at national level for use in policy and research. In a pilot project, the indexing and merging of SEE data from 2015-2019 was tested in collaboration with six federal states. This was done using obesity prevalence at the time of the school entrance examination. In addition, prevalences were linked to small-scale indicators on settlement structure and sociodemographics from public databases, differences in obesity prevalence at county level were identified, and correlations to regional influencing factors were visualised. It was feasible to merge SEE data from the federal states with little effort. The majority of the selected indicators were freely available in public databases. In an interactive, easily comprehensible and user-friendly Tableau dashboard for visualising the SEE data, it can be seen that obesity prevalences differ significantly between counties that are similar in terms of settlement structure or sociodemographics. Providing federal state SEE data and linking them to small-scale indicators enables region-based analyses and cross-state comparisons of similar counties and provides a data basis for continuous monitoring of the prevalence of obesity in early childhood.

Artificially sentient beings: Moral, political, and legal issues

The emergence of artificially sentient beings raises moral, political, and legal issues that deserve scrutiny. First, it may be difficult to understand the well-being elements of artificially sentient beings and theories of well-being may have to be reconsidered. For instance, as a theory of well-being, hedonism may need to expand the meaning of happiness and suffering or it may run the risk of being irrelevant. Second, we may have to compare the claims of artificially sentient beings with the claims of humans. This calls for interspecies aggregation, which is a neglected form of interpersonal aggregation. Lastly, there are practical problems to address, such as whether to include artificially sentient beings in the political decision-making processes, whether to grant them a right to self-determination in digital worlds, and how to protect them from discrimination. Given these, the emergence of artificially sentient beings compels us to reevaluate the positions we typically hold.

Olivine—The Little Green Science Machine

In some ways, olivine has driven the evolution of the Solar System and likely beyond. As one of the earliest-crystallizing silicate minerals, olivine controls the initial chemical evolution of planet-wide magma oceans and individual lava flows alike. In solid aggregate form, it controls and records deformation of the mantle and smaller-scale intrusive complexes. The components of its crystal structure are mobile at high temperatures and their migration can be used to explore the timing of magmatic events. During chemical weathering, these olivine crystals capture carbon dioxide from the atmosphere as secondary minerals are formed. All of these processes take place not only on Earth, but also on other planetary bodies, making olivine ideally suited to shed light on both primordial planet-building processes and current-day volcanism and surface processes.

Accounting for carbon emission rights: China’s experience

The article is devoted to the modern Chinese experience in accounting for carbon rights in the context of the active implementation of low-carbon economic development practices both at the national and international levels. The methodological basis of the work is the main regulatory legal acts of the People’s Republic of China that regulate the accounting of rights to carbon emissions and carbon trading, scientific research by Chinese authors on the main problems and tasks of national accounting of carbon rights, accounting practices of key Chinese enterprises in the energy sector. On this basis, the main theoretical aspects of accounting for rights to carbon emissions are highlighted, which are the subject of active scientific discourse in China at the present stage: the goals of carbon accounting, subject affiliation, features of information disclosure. Based on the main provisions of current regulations and an analysis of the accounting practices that have developed over the past 7 years of key Chinese enterprises in the industry, the modern accounting practices of carbon rights and financial reporting disclosures are presented in a concise form: metric properties, main involved accounts of the National Chart of Accounts of China, information to be disclosed in the notes to the financial statements. The study is crowned by the identified main problems of the modern Chinese practice of accounting for carbon rights in an aggregated form and the proposals formulated by the author. The results of the work contribute to the theory of low-carbon accounting, more specifically, the approaches of scientists are presented, and also provide the Russian reader with the opportunity to get acquainted with the accounting practice of carbon rights in China — in the country that makes the most significant “contribution” to the processes of environmental pollution in the global scale. The the author’s reliance on on authentic sources in Chinese is of particular value to the work, which reveal the thoughts, ideas, practices that are inaccessible to a wide range of readers.

Polymerization of tetrazine-substituted diacetylenes as aggregates in suspension.

Polydiacetylenes (PDAs) are conjugated polymers that have been widely exploited for their chromogenic and fluorogenic transitions upon exposure to external stimuli and biomolecules of interest. Herein, we propose a comparative study of the polymerization dynamics of two diacetylene derivatives, TzDA1 and TzDA2, in the form of aggregates in suspension prepared by reprecipitation method from organic solvents in water, varying the diacetylene concentration and solvent proportions, and sonication in water, varying the time and temperature. Both derivatives bear a tetrazine fluorophore, which serves both to increase the fluorescence quantum yield of the system and to track the polymerization by fluorescence quenching exclusively by the blue-PDA, and differ by the chain termination. It was shown that adding a butyl ester function in TzDA2 to a simple urethane (TzDA1) influences the polymerizability and kinetics of polymerization of the aggregates in suspension. In addition, we showed that also the preparation method and preparation conditions do have an influence on the polymerization dynamics, suggesting that a careful study of these properties should be carried out before investigating the applications of such objects.

Formation of amyloid loops in brain tissues is controlled by the flexibility of protofibril chains

Neurodegenerative diseases, such as Alzheimer's disease (AD), are associated with protein misfolding and aggregation into amyloid fibrils. Increasing evidence suggests that soluble, low-molecular-weight aggregates play a key role in disease-associated toxicity. Within this population of aggregates, closed-loop pore-like structures have been observed for a variety of amyloid systems, and their presence in brain tissues is associated with high levels of neuropathology. However, their mechanism of formation and relationship with mature fibrils have largely remained challenging to elucidate. Here, we use atomic force microscopy and statistical theory of biopolymers to characterize amyloid ring structures derived from the brains of AD patients. We analyze the bending fluctuations of protofibrils and show that the process of loop formation is governed by the mechanical properties of their chains. We conclude that ex vivo protofibril chains possess greater flexibility than that imparted by hydrogen-bonded networks characteristic of mature amyloid fibrils, such that they are able to form end-to-end connections. These results explain the diversity in the structures formed from protein aggregation and shed light on the links between early forms of flexible ring-forming aggregates and their role in disease.

Yeast Chaperone Hsp70-Ssb Modulates a Variety of Protein-Based Heritable Elements.

Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates (mnemons) are frequently based on cross-β ordered fibrous aggregates (amyloids). The formation and propagation of yeast prions are controlled by chaperone machinery. Ribosome-associated chaperone Hsp70-Ssb is known (and confirmed here) to modulate formation and propagation of the prion form of the Sup35 protein [PSI+]. Our new data show that both formation and mitotic transmission of the stress-inducible prion form of the Lsb2 protein ([LSB+]) are also significantly increased in the absence of Ssb. Notably, heat stress leads to a massive accumulation of [LSB+] cells in the absence of Ssb, implicating Ssb as a major downregulator of the [LSB+]-dependent memory of stress. Moreover, the aggregated form of Gγ subunit Ste18, [STE+], behaving as a non-heritable mnemon in the wild-type strain, is generated more efficiently and becomes heritable in the absence of Ssb. Lack of Ssb also facilitates mitotic transmission, while lack of the Ssb cochaperone Hsp40-Zuo1 facilitates both spontaneous formation and mitotic transmission of the Ure2 prion, [URE3]. These results demonstrate that Ssb is a general modulator of cytosolic amyloid aggregation, whose effect is not restricted only to [PSI+].

Front Cover: Chiral Diketopyrrolo[3,4‐c]pyrrole‐1,2,3‐1H‐triazole Dyes with Highly Tuneable Properties in Solution and Thin Films (Chem. Eur. J. 34/2023)

Supramolecular chirality is far from being determined only by local stereogenic elements. Three diketopyrrolo[3,4-c]pyrrole–1,2,3-1H-triazole (DPP) dyes bearing the same chiral appendage R* but decorated with different achiral substituent groups Y showed profoundly different optical, chiroptical, electrochemical and thermal features in their aggregated form. More information can be found in the Research Article by A. Punzi, L. Di Bari and co-workers (DOI: 10.1002/chem.202300291).

Structure-from-Motion Photogrammetry and Rare Earth Oxides can quantify diffuse and convergent soil loss and source apportionment

Accurately quantifying rates of soil erosion requires capturing both the volumetric nature of the visible, convergent fluvial pathways (also known as rills) and the subtle nature of the less-visible, diffuse pathways (interrill areas). The aim of this study was to use Rare Earth Oxide (REO) tracers and Structure-from-Motion (SfM) photogrammetry to elucidate retrospective information about soil erosion rates and sediment sources during different soil erosion conditions, within a controlled laboratory environment. The experimental conditions created erosion events consistent with diffuse and convergent erosion processes. REO tracers allowed the sediment transport distances of over 2 m to be described, and helped resolved the relative contribution of diffuse and convergent soil erosion; interrill areas were also identified as a significant sediment sources soil loss under convergent erosion conditions. While the potential for SfM photogrammetry to resolve sub-millimetre elevations changes was demonstrated, under some conditions non-erosional changes in surface elevation, such as compaction, exceeded volumes of soil loss via diffuse erosion. The discrepancies between SfM Photogrammetry calculations and REO tagged sediment export were beneficial, identifying that during soil erosion events sediment in both aggregate and particle form is deposited within the convergent features, even when the rill extended the full length of the soil surface. The combination of SfM photogrammetry and REO tracers has provided a novel platform for building a spatial understanding of patterns of soil loss and source apportionment between rill and interrill erosion.

A frame of understanding to better link nature-based solutions and urban planning

Reinforcement of the concept of nature-based solutions in urban environments calls for their better introduction and linkage into urban planning. The paper is focused on the relationship between nature-based solutions and spatial realities, based on reciprocity among natural processes and urban patterns, emphasising the recognition of using and mimicking natural processes in urban environments. A classification framework as a form of knowledge aggregation is suggested. A matrix that simultaneously addresses the role of natural processes in nature-based solutions and the ability of such processes to deliver results for improving urban environments is proposed. Accordingly, there are three characteristic groups of solutions suggested, (1) those only using natural processes, (2) those using and mimicking natural processes and (3) those only mimicking natural processes, which implementation potentials are commented against four different types of urban patterns, to show what group of the nature-based solutions may best suit any type of spatial agglomeration. Beside green infrastructure as currently the most often addressed manifestation of nature-based solutions in cities, the paper reflects also on the physical processes as inevitable parts of nature. In relation to urban planning, sites and their characteristics are seen as a crucial aspect of nature-based solutions. The arguments are built upon exhaustive literature and case studies review, resulted in the matrix showing the matching relations among nature-based solutions and societal challenges aiming for better urban environment. Additionally, there are also sets of recommendations for bridging the policy-implementation gaps to bring nature-based solutions closer to urban planning, suggested.

Dieter Wolf (1941–2023): a life dedicated to understanding protein quality control and the ubiquitin‐proteasome system

Dieter Wolf (1941–2023): a life dedicated to understanding protein quality control and the ubiquitin‐proteasome system

Impact of Natural Pozzolan and the Degree of Circularity of Aggregates on the Thickness, Strength and Durability of ITZ in Concrete (Modeling and Experimentation)

The interfacial transition zone (ITZ) has a significant negative impact on the structural performance of concrete. This negative impact can be ameliorated by introducing mineral additions into the concrete. In this study, different forms (degree of circularity) of coarse aggregates and three contents (10 %, 15 % and 20 %) of mineral addition (natural pozzolan) were used to prepare ordinary concrete. This article aims to determine the optimal and effective mixture (the best form of aggregate and addition). This article aims to determine the optimal and efficient mixture (the best form of aggregate and addition) on the basis of mechanical (compressive strength), and chemical (immersion in 3.5 % H2SO4 solution) tests. Furthermore, the effect of the interaction between the aggregate and the modified cementitious matrix was analyzed and discussed using the scanning electron microscope (SEM). The results show that the effect of the addition of 20 % pozzolana improves the aggregate/matrix transition zone, which made it possible to develop a maximum compressive strength at 60 days (51 MPa). In addition, the effect of mineral additions varies depending on the shape of the coarse aggregate. Thus, an effective numerical modeling of the compressive strength is based on the approach of the full factorial design taking into account the degree of circularity of the coarse aggregates and the content of the pozzolan.

Chiral diketopyrrolo[3,4-c]pyrrole-1,2,3-1H-triazole dyes with highly tunable properties in solution and thin films.

We studied the impact of achiral substituents on the chiral supramolecular architectures of diketopyrrolo[3,4-c]pyrrole-1,2,3-1H-triazole (DPP) dyes. We decorated the same chiral DPP motif with substituent groups on the nitrogen atoms of the lactam moiety: the hydrophobic n-octyl alkyl chain, the hydrophilic triethylene glycol (TEG) chain and the thermo-cleavable t-butoxycarbonyl (t-Boc) carbamate group. In spite of identical conjugated chromophore and chiral appendage, in aggregated form the three dyes displayed profoundly different optical, chiroptical, electrochemical and thermal features. ECD measurements revealed differences in the aggregation modes, which would be inaccessible by most other techniques. We found strong chiroptical features, which would have major implications in the context of chiral organic opto-electronics and in the development of other highly innovative technological applications.

Reducing α-Synuclein in Human CSF; An Evaluation of Safety, Tolerability, Pharmacokinetics and Pharmacodynamics of MEDI1341, an α-Synuclein-specific antibody, in Healthy Volunteers and Parkinson’s Disease Patients (P1-11.007)

<h3>Objective:</h3> To evaluate the safety, tolerability, pharmacokinetics (PK) and pharmacodynamics (PD) of MEDI1341 (TAK-341) in single (SAD; NCT03272165) and multiple ascending dose (MAD; NCT04449484) studies undertaken in healthy volunteers (HVs) and Parkinson’s disease patients, respectively. <h3>Background:</h3> MEDI1341 is a human IgG1λ monoclonal antibody, engineered for selective, high-affinity binding of α-synuclein (ASN) and for reduced effector function. MEDI1341 recognises both monomeric and aggregated forms of human ASN. In rats and cynomolgus monkeys, MEDI1341 decreases free ASN in brain interstitial fluid and cerebrospinal fluid (CSF). In a mouse model, MEDI1341 attenuates ASN axonal propagation and accumulation in the brain. <h3>Design/Methods:</h3> HVs aged 18–80 years were eligible for the SAD study. Subjects eligible for the MAD study were aged 40–85 years with a diagnosis of mild-moderate Parkinson’s disease according to the UK Parkinson’s Disease Society Brain Bank criteria and stage 1–3 on the Hoehn and Yahr scale. In the SAD study, N=49 subjects received placebo or MEDI1341 administered intravenously (IV) across six dose levels. In the MAD study, two dose levels were evaluated in Parkinson’s patients (N=25), administered IV every 4 weeks for 3 infusions. <h3>Results:</h3> Administration of MEDI1341 or placebo to HVs or Parkinson’s patients was not associated with any medically important changes in safety parameters across all doses tested. Dose-dependent changes in serum concentrations for MEDI1341 were observed across cohorts. CSF concentrations demonstrated central nervous system penetration of MEDI1341. PD data showed dose-dependent suppression of free ASN in CSF, consistent with the results seen in preclinical species. <h3>Conclusions:</h3> MEDI1341 was generally well tolerated following IV administration to HVs or Parkinson’s patients after single or repeat doses, respectively. The PK and PD data provide evidence of dose-dependent and selective ASN target engagement by MEDI1341 in the central compartment. Full study design and data from the Phase 1 studies will be presented. <b>Disclosure:</b> Dr. Shering has received personal compensation for serving as an employee of AstraZeneca. An immediate family member of Dr. Shering has received personal compensation for serving as an employee of eResearch Technology Inc. Dr. Shering has stock in AstraZeneca. Dr. Shering has received intellectual property interests from a discovery or technology relating to health care. Michael Pomfret has nothing to disclose. Dr. Kubiak has received personal compensation for serving as an employee of AstraZeneca. Dr. Kubiak has stock in AstraZeneca. Mrs. Pouliquen has received personal compensation for serving as an employee of AstraZeneca. Mrs. Pouliquen has received personal compensation for serving as an employee of GSK. Mrs. Pouliquen has stock in GSK. Mrs. Pouliquen has stock in AstraZeneca. Wei Yin has received personal compensation for serving as an employee of Takeda. Wei Yin has stock in Takeda. Arthur Simen has received personal compensation for serving as an employee of Takeda. Dr. Ratti has received personal compensation for serving as an employee of Takeda. Dr. Ratti has received personal compensation for serving as an employee of Biogen. Dr. Ratti has stock in Takeda. Dr. Ratti has stock in Biogen. Dr. Perkinton has stock in AstraZeneca. Dr. Tan has received personal compensation for serving as an employee of AstaZeneca. An immediate family member of Dr. Tan has received personal compensation in the range of $50,000-$99,999 for serving as a Consultant for SOBI. Dr. Tan has stock in AstraZeneca. Dr. Chessell has received personal compensation in the range of $100,000-$499,999 for serving as a Employee with AstraZeneca. Dr. Ostenfeld has received personal compensation for serving as an employee of AstraZeneca. Dr. Ostenfeld has stock in AstraZeneca. Dr. Ostenfeld has received intellectual property interests from a discovery or technology relating to health care.