Ricardo L. Mancera's research while affiliated with Curtin University and other places
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Publications (186)
Fungal effector proteins are important in mediating disease infections in agriculturally important crops. These secreted small proteins are known to interact with their respective host receptor binding partners in the host, either inside the cells or in the apoplastic space, depending on the localisation of the effector proteins. Consequently, it i...
Surface lipids influence the biological activities of high-density lipoproteins (HDLs) but their species-specific effects on HDL structure, dynamics, and surface interactome has remained unclear. Building upon the five-lipid species HDL models developed and characterised in previous work, representative models of the major HDL subpopulations found...
Pathogenic fungal diseases in crops are mediated by the release of effector proteins that facilitate infection. Characterising the structure of these fungal effectors is vital to understanding their virulence mechanisms and interactions with their hosts, which is crucial in the breeding of plant cultivars for disease resistance. Several effectors h...
The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is...
The use of pH indicators provides a simple, semi-quantitative visual method for quickly assessing pH changes in tissue culture media; however, pH indicators are rarely used in routine plant tissue culture media. In this study, chlorophenol red, bromocresol purple, and bromocresol green were tested to assess their functionality in the growth medium...
The barrier imposed by the outer layer of the skin, the stratum corneum, creates an almost impermeable environment for exogenous substances. Few lipophilic drugs with low molecular mass can passively diffuse through this layer, highlighting the need to develop methods to enable the delivery of more drugs via the transdermal route. The prodrug appro...
The Myrtaceae is one of the largest plant families present in Australia and is dominant both structurally and floristically in many diverse ecosystems. Many species are also valuable for the resources they provide, such as timber, oils, and fruits. However, Myrtaceae species in Australia are threatened by Myrtle Rust and in urgent need of conservat...
Background:
Novel cryo-techniques are continuously being developed that may better improve cryogenic survival in plants, with the aim of reducing exposure times to otherwise toxic cryoprotective agents whilst maximising regeneration rates.
Objective:
This study used cryo-mesh and vacuum infiltration vitrification with two vitrification solutions...
Cryopreservation allows the long-term storage of plant germplasm, but can cause damage to plant tissues, which must be repaired for survival to occur. This repair process is fuelled by the metabolic function of mitochondria; however, little is known about how metabolic function is affected by the cryopreservation process in plants. We compared meta...
Intrinsically disordered peptides, such as amyloid β42 (Aβ42), lack a well-defined structure in solution. Aβ42 can undergo abnormal aggregation and amyloidogenesis in the brain, forming fibrillar plaques, a hallmark of Alzheimer's disease. The insoluble fibrillar forms of Aβ42 exhibit well-defined, cross β-sheet structures at the molecular level an...
The local intermolecular structure and related dynamics in the liquid cis-trans N-methylformamide mixture at ambient temperature and density conditions have been systematically studied by employing Born-Oppenheimer molecular dynamics simulation techniques. Particular attention has been paid to the local structure around the cis- and trans- conforme...
Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein (IDP) whose abnormal aggregation into toxic soluble oligomers and insoluble amyloid fibrils is a pathological feature in type‐2 diabetes. Rat IAPP (rIAPP) differs from hIAPP by only six amino acids yet has a reduced tendency to aggregate or form fibri...
Aggregation of amyloid beta into amyloid plaques in the brain is a hallmark characteristic of Alzheimer's disease. Therapeutics aimed at preventing or retarding amyloid formation often rely on detailed characterization of the underlying mechanism and kinetics of protein aggregation. Surface plasmon resonance (SPR) spectroscopy is a robust technique...
The local intermolecular structure and related dynamics in the liquid cis/trans N-methylformamide mixture at ambient temperature and density conditions have been systematically studied by employing Born-Oppenheimer molecular dynamics simulation techniques. Particular attention has been paid to the local structure around the cis- and trans- conforme...
The Myrtaceae is a very large and diverse family containing a number of economically and ecologically valuable species. In Australia, the family contains approximately 1700 species from 70 genera and is structurally and floristically dominant in many diverse ecosystems. In addition to threats from habitat fragmentation and increasing rates of natur...
Background:
Type 2 diabetes related human islet amyloid polypeptide (hIAPP) plays a dual role in Alzheimer's disease (AD). hIAPP has neuroprotective effects in AD mouse models whereas, high hIAPP concentrations can promote co-aggregation with amyloid-β (Aβ) to promote neurodegeneration. In fact, both low and high plasma hIAPP concentration has bee...
CRYO2021 Conference Abstract
Cryopreservation is a valuable tool for the long-term storage of important in vitro cultures, both for species of conservation importance and of economic value. However, it is well known that cryopreservation imposes a range of potentially damaging stresses on samples, including temperature stress, osmotic stress, toxic...
CRYO2021 Conference Abstract
Macadamia integrifolia and M. tetraphylla are small rainforest trees native to the east coast of Australia. Cultivars of the species are prized for their nuts and grown in plantations with high economic value both in Australia and overseas; however, both species are threatened in their natural habitat. Although Macadami...
Cryopreservation has several advantages over other ex situ conservation methods, and indeed is the only viable storage method for the long term conservation of most plant species. However, despite many advances in this field, it is increasingly clear that some species are ill-equipped to overcome the intense stress imposed by the cryopreservation p...
Fungal plant-pathogens promote infection of their hosts through the release of ‘effectors’—a broad class of cytotoxic or virulence-promoting molecules. Effectors may be recognised by resistance or sensitivity receptors in the host, which can determine disease outcomes. Accurate prediction of effectors remains a major challenge in plant pathology, b...
SOX2 is an oncogenic transcription factor overexpressed in nearly half of the basal-like triple-negative breast cancers associated with very poor outcomes. Targeting and inhibiting SOX2 is clinically relevant as high SOX2 mRNA levels are positively correlated with decreased overall survival and progression-free survival in patients affected with br...
Metabolic diseases, such as obesity and type 2 diabetes, are relentlessly spreading worldwide. The beginning of the 21st century has seen the introduction of mechanistically novel types of drugs, aimed primarily at keeping these pathologies under control. In particular, an important family of therapeutics exploits the beneficial physiology of the g...
ACE2 has been established as the main receptor for SARS-CoV-2. Since other human coronaviruses are known to use co-receptors for viral cell entry, it has been suggested that DPP4 (CD26) could be a potential additional binding target or co-receptor, supported by early molecular docking simulation studies. However, recent biophysical studies have sho...
BZD9L1 was previously described as a SIRT1/2 inhibitor with anti-cancer activities in colorectal cancer (CRC), either as a standalone chemotherapy or in combination with 5-fluorouracil. BZD9L1 was reported to induce apoptosis in CRC cells; however, the network of intracellular pathways and crosstalk between molecular players mediated by BZD9L1 is n...
‘Effectors’ are a broad class of cytotoxic or virulence-promoting molecules that are released from plant-pathogen cells to cause disease in their host. Fungal effectors are a core research area for improving host disease resistance; however, because they generally lack common distinguishing features or obvious sequence similarity, discovery of effe...
The bunya pine (Araucaria bidwillii Hook., family Araucariaceae) isendemic to Queensland in eastern Australia, where only two fragmentedpopulations remain. Cones were collected from the Australian BotanicGarden Mount Annan and the Royal Botanic Gardens Sydney. Seed em-bryos with cotyledon tubes excised were sown on water agar or basalmedium contain...
Human serum high-density lipoproteins (HDLs) are a population of small, dense protein-lipid aggregates that are crucial for intravascular lipid trafficking and are protective against cardiovascular disease. The spheroidal HDL subfraction can be separated by size and density into five major subpopulations with distinct molecular compositions and uni...
The human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transporter with the highest quality us...
Cell membranes protect and compartmentalise cells and their organelles. The semi‐permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotec...
High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that triggers the progression of several pro-inflammatory diseases such as diabetes, Alzheimer’s disease and cancer, by inducing signals upon interaction with the receptors such as the receptor for advanced glycation end-products (RAGE) and toll-like receptor...
Melittin is an anti-microbial peptide (AMP) and one of the most studied membrane-disrupting peptides. There is, however, a lack of accurate measurements of the concentration-dependent kinetics and affinity of binding of melittin to phospholipid membranes. In this study, we used surface plasmon resonance spectroscopy to determine the concentration-d...
Sugar-membrane interactions are believed to be responsible for cell preservation during desiccation and freezing, but the molecular mechanism by which they achieve this is still not well understood. The associated decrease of the main phase transition temperature of phospholipid bilayers is explained by two opposing views on the matter: the direct...
The cross‐strand disulfides (CSDs) found in β‐hairpin antimicrobial peptides (β‐AMPs) show a unique disulfide geometry that is characterised by unusual torsion angles and a short Cα‐Cα distance. While the sequence and disulfide bond connectivity of disulfide‐rich peptides is well studied, much less is known about the disulfide geometry found in CSD...
The cytoplasm is a densely packed environment filled with macromolecules with hindered diffusion. Molecular simulation of the diffusion of biomolecules under such macromolecular crowding conditions requires the definition of a simulation cell with a cytoplasmic-like composition. This has been previously done for prokaryote cells (E. coli) but not f...
Protein electrochemistry studies at the polarized interface between two immiscible electrolyte solutions (ITIES) indicate that the detection mechanism of the protein at the interface involves a combination of protein-anion complexation and interfacial adsorption processes. Detailed characterisation of the protein-facilitated mechanism of ion transf...
Eighteen native species of Nymphaea (waterlilies) inhabit a range of freshwater wetlands in northern Australia, which are threatened by increased development and the potential impacts of climate change. To investigate conservation seed banking of these vulnerable species, we aimed to characterize their seed storage physiology by determining (i) see...
The electroadsorption of proteins at aqueous-organic interfaces offers the possibility to examine protein structural rearrangements upon interaction with lipophilic phases, without modifying the bulk protein or relying on a solid support. The aqueous-organic interface has already provided a simple means of electrochemical protein detection, often i...
An alarming proportion of Australia's unique plant biodiversity is under siege from a variety of environmental threats. Options for in situ conservation are becoming increasingly compromised as encroaching land use, climate change and introduced diseases are highly likely to erode sanctuaries regardless of best intentions. Ex situ conservation is c...
Xanthine oxidase (XO) is the enzyme responsible for the catabolism of purines and their conversion into uric acid. XO is thus the target for the treatment of hyperuricemia and gout. For more than 50 years the only XO inhibitor drug available on the market was the purine analogue allopurinol. In the last decade there has been a resurgence in the sea...
Biophysical studies of model cell membranes at full and low hydration are usually carried out using scattering measurements on multi-bilayer systems. Molecular simulations of lipid bilayers aimed at reproducing those experimental conditions are usually conducted using single bilayers with different amounts of water. These simulation conditions may...
The adsorption of proteins at aqueous-organic interfaces offers the possibility to examine protein structural rearrangements upon interaction with lipophilic phases, without modifying the bulk protein or relying on a solid support. The aqueous-organic interface has already provided a simple means of protein detection, often involving adsorption and...
The integrity of mitochondrial function within cells is essential for the successful recovery of cryopreserved material but there has been very limited investigation in plants. Mitochondria are the energy production facility in cells, producing adenosine triphosphate (ATP) through the electron transport chain, as well as carbon skeletons required i...
Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The soluble, oligomeric forms of hIAPP are the most...
The electrochemistry of proteins at the interface between two immiscible electrolyte solutions (ITIES) is discussed, with detection capabilities based on protein-facilitated anion transfer, and which has enabled protein detection via adsorptive stripping voltammetry. Targeting an enzymatic biomarker has achieved detection at picomolar concentration...
This review summarises the current knowledge of Gomesin (Gm), an 18-residue long, cationic anti-microbial peptide originally isolated from the haemocytes of the Brazilian tarantula Acanthoscurria gomesiana. The peptide shows potent cytotoxic activity against clinically relevant microbes including Gram-positive and Gram-negative bacteria, fungi, and...
Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecula...
Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses...
The neural-specific transcription factor Engrailed 1 - is overexpressed in basallike breast tumours. Synthetic interference peptides - comprising a cell-penetrating peptide/nuclear localisation sequence and the Engrailed 1-specific sequence from the N-terminus have been engineered to produce a strong apoptotic response in tumour cells overexpressin...
T-cell epitopes are specific peptide sequences derived from foreign or own proteins that can initiate an immune response and which are recognized by specific T-cells when displayed on the surface of other cells. The prediction of T-cell epitopes is of particular interest in vaccine design, disease prevention and the development of immunotherapeutic...
The beta amyloid protein (Aβ) plays a central role in Alzheimer's disease (AD) pathogenesis and its interaction with cell membranes in known to promote mutually disruptive structural perturbations that contribute to amyloid deposition and neurodegeneration in the brain. In addition to protein aggregation at the membrane interface and disruption of...
The Tasmanian devil faces extinction due to devil facial tumour disease (DFTD), a highly transmittable clonal form of cancer without available treatment. In this study, we report the cell-autonomous antiproliferative and cytotoxic activities exhibited by the spider peptide gomesin (AgGom) and gomesin-like homologue (HiGom) in DFTD cells. Mechanisti...
The Tau protein plays an important role due to its biomolecular interactions in neurodegenerative diseases. The lack of stable structure and various posttranslational modifications such as phosphorylation at various sites in the Tau protein pose a challenge for many experimental methods that are traditionally used to study protein folding and aggre...
Key message Three wild species exhibited a significant reduction in antioxidants throughout the cryopreservation protocol, whilst the half-cell reduction potential became more oxidised. Antioxidant content recuperated in recovering shoot tips.
Abstract Cryopreservation is the most efficient and cost effective long-term storage solution for the
co...
The insulin signalling system is one of the most conserved endocrine systems of Animalia from mollusc to man. In decapod Crustacea, such as the Eastern spiny lobster, Sagmariasus verreauxi (Sv) and the red-claw crayfish, Cherax quadricarinatus (Cq), insulin endocrinology governs male sexual differentiation through the action of a male-specific, ins...
The Gaussian-based 3D-QSAR studies for 58 selective COX-2 (cyclooxygenase-2) inhibitors belonging to benzopyran chemical class were performed. Partial least squares analysis produced statistically significant model with (R training 2 = 0.866) and predictability (Q training 2 = 0.66, Q test 2 = 0.846). The 3D-QSAR model includes steric, electrostati...
Australia is host to an amazing diversity of species, many of which require conservation efforts. In vitro culture provides a tool for not only conserving these threatened species but allows for their propagation from limited starting material. Cryopreservation provides the greatest long-term storage option for in vitro cultures and as a conservati...
While well established for studying the internal structure of bilayers and orientation of peptides and proteins with respect to bilayers, neutron lamellar diffraction is also a powerful tool for studying the average locus of solubilisation of small molecules in stacks of lipid bilayers. The approach has provided unique insights into important issue...
Cholesterol oxidase (ChOx) is a flavoenzyme that oxidises and isomerises cholesterol (CHL) to form cholest-4-en-3-one. Molecular docking and molecular dynamics simulations were conducted to predict the binding interactions of CHL in the active site. Several key interactions (E361-CHL, N485-FAD and H447-CHL) were identified and which are likely to d...
BRAF mutation testing to determine eligibility for treatment with vemurafenib was performed on archival skin lesions of a 54-year-old patient diagnosed with Erdheim–Chester disease (ECD) in 1999. Sanger sequencing of DNA extracted from a 2008 skin lesion identified two non-contiguous base substitutions in BRAF, which were shown by next-generation s...
Background:
The continued development of new cryopreservation protocols has improved post-cryogenic success rates for a wide variety of plant species. Methods like the cryo-plate have proven beneficial in simplifying the cryopreservation procedure.
Objective:
This study assessed the practicality of a stainless steel mesh strip (cryo-mesh) for cr...
The anti-cancer activity of the benzo[h]quinolines was evaluated on cultured human skin cancer (G361), lung cancer (H460), breast cancer (MCF7) and colon cancer (HCT116) cell lines. The inhibitory effect of these compounds on the cell growth was determined by the MTT assay. The compounds 3e, 3f, 3h and 3j showed potential cytotoxicity against these...
HMGB1, a chromatin protein, interacts with DNA and controls gene expression. However, when HMGB1 is released from apoptotic or damaged cells it triggers pro-inflammatory reactions by interacting with various receptors, mainly RAGE and TLRs. The self-association of HMGB1 has been found to be crucial for its DNA-related biological functions. It is in...
Australia contains many unique and highly endemic ecosystems, with a large number of rare and threatened species. Cryopreservation of these plants provides the safest long-term conservation approach, however success rates post-cryopreservation vary largely between plant species. A deeper understanding of the stresses experienced during the cryopres...
There have been multiple advances in cryopreservation protocols for conserving plant germplasm, including vitrification, droplet vitrification, encapsulation dehydration, encapsulation vitrification and more recently vacuum infiltration vitrification and cryo-plate protocols. The cryo-plate technique has delivered benefits for the cryopreservation...
The aberrant epigenetic silencing of tumor suppressor genes (TSGs) plays a major role during carcinogenesis and regaining these dormant functions by engineering of sequence-specific epigenome editing tools offers a unique opportunity for targeted therapies. However, effectively normalizing the expression and regaining tumor suppressive functions of...
Paired helical filaments (PHFs) resulting from the hyperphosphorylation of the protein tau are major components of the Alzheimer disease. They contribute to the formation of intraneuronal neurofibrillary tangles. Accordingly, the phosphorylation of the serine 202 (Ser-202) and the threonine 208 (Thr-208) seem relatively specific. These two residues...
The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc–protein association is essential to improve our understanding of the immune system at the molec...
HMGB1 triggers proinflammatory reactions by interacting extracellularly with various receptors. HMGB1 also acts in the nucleus by interacting with DNA and controlling DNA transcription, a process which involves its self-association. The self-association of HMGB1 was characterized using surface plasmon resonance (SPR). A dimer/tetramer binding model...
Poster presented at the CRYO2016 conference
Lomandra sonderi (Asparagaceae) is endemic to the south-west Western Australian Jarrah (Eucalyptus marginata) forest region and is a difficult to propagate species important to post-mining restoration. Micropropagation is the only way to currently produce plants of this species for restoration. This study describes investigations into optimising cr...
Micropropagation and cryopreservation protocols were developed for the threatened Australian species Androcalva perlaria. Vegetative shoots were brought into culture using a simplified surface sterilisation process with between 26 and 100 % of shoots successfully initiated across all genotypes. Shoots were multiplied on ½ MS basal salts medium (BM)...
The adsorption of proteins at the interface between two immiscible electrolyte solutions (ITIES) has been found to be key to their bioelectroactivity at such interfaces. Combined with interfacial complexation of organic phase anions by cationic proteins, this adsorption process may be exploited to achieve nanomolar protein detection. In this study,...
Surface plasmon resonance (SPR) is a powerful technique for evaluating protein-protein interactions in real time. However, inappropriately optimised experiments can often lead to problems in the interpretation of data, leading to unreliable kinetic constants and binding models. Optimisation of SPR experiments involving “sticky” proteins, or protein...
Previously we determined using neutron membrane diffraction the density profile of solute molecules confined between lipid bilayers. This was to understand the mode of action of small solutes (sugars) as cryoprotectants (1, 2). The interlamellar profile of sugars differs with those determined indirectly from molecular dynamics simulations(3) but th...
Paired helical filaments (PHFs) resulting from the hyperphosphorylation of the protein tau are major components of the Alzheimer disease. They contribute to the formation of intraneuronal neurofibrillary tangles. Accordingly, the phosphorylation of the serine 202 (Ser-202) and the threonine 208 (Thr-208) seem relatively specific. These two residues...
Post mortem biochemical staging of Alzheimer's disease is currently based on immunochemical analysis of brain slices with the AT8 antibody. The epitope of AT8 is described around the pSer202 /pThr205 region of the hyperphosphorylated form of the neuronal protein tau. In this study, NMR spectroscopy was used to precisely map the AT8 epitope on phosp...
Background:
The application of a vacuum during the incubation in cryoprotective agents such as PVS2 allows for increased penetration, reducing total incubation times required before vitrification and post-cryopreservation regeneration is achieved.
Objective:
This study compared a conventional droplet-vitrification protocol to the new vacuum infi...
There is limited knowledge of the effects of exposure to low temperatures in the unique Mediterranean climate plant species of Western Australia. We have thus investigated the effect of low temperature on cryogenic tolerance in Lomandra sonderi, an endemic perennial species of southwest Western Australia. Lomandra sonderi plants were preconditioned...
Graphical abstract
The global aromaticity and π aromaticity of the classic heterobenzenes (C6H6 > C5H5N > C5H5P > C5H5As > C5H5Sb > C5H5Bi) is established firmly. For σ aromaticity, the technique of ELFσ permits overall assignment of σ aromatic character of the group five heterobenzenes. Both FLFπ and NICS(max)πzz are easily and efficiently applied...
Aggregation of the microtubule associated protein tau (MAPT) within neurons of the brain is the leading cause of tauopathies such as Alzheimer's disease. MAPT is a phospho-protein that is selectively phosphorylated by a number of kinases in vivo to perform its biological function. However it may become pathogenically hyperphosphorylated, causing ag...
Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1 (AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics (MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of for...
Citations
... MSD∼ t α , as observed in amorphous materials [20][21][22][23][24][25][26][27][28], biological * dansh5d@gmail.com † stasbur@gmail.com cells [6,8,[29][30][31][32][33], granular materials [10,34,35], non-Newtonian fluids [36] and other systems [37][38][39]. These power-law distributed waiting times (∼ τ −(1+α) ), as detected in various systems [9,36,[40][41][42], can appear naturally due to the exponential distribution of the depths of energetic wells that give rise to the regions of local arrest. ...
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... Table 6.1;Hardstaff et al. 2020; Hamilton et al. 2013;Sommerville et al. 2021). ...
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... High RMSd_i values result from significant alterations in the structure of one monomer when it binds [83]. The fraction of common contacts (Fnat) represents the proportion of native interfacial interactions that remain in the predicted docked complex's interface in comparison to the experimental complex structure [84]. A higher Fnat value indicates that a large proportion of native contacts is maintained, while a lower Fnat value signifies the loss of native contacts, which might lead to loss of function or altered biological activity [41]. ...
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... Similar observations were made in other recent studies where experimentally resolved structures of fungal effectors were compared with AF2 predictions, as for example in the case of LARS [46], FOLD [47] and RALPH [48] effectors. Comparison with a published study testing ab initio approaches using Rosetta or the two web servers Robetta and QUARK to model MAX effectors with already known structures [49] confirmed that AF2 outcompetes other strategies for the prediction of MAX effector structures. ...
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... For these analyses eight experimental structures of MAX effectors were used as templates for homology modeling, and as a training data set for the TM-pred scoring function [11]. To improve the accuracy of template-query alignments that is crucial for obtaining accurate predicted models as indicated in [19] we have implemented a bidirectional dynamic programming algorithm described in [11] exploring many sub-optimal alignments which where assessed using complementary structural scoring methods. Almost 90% of the OG proteins were modeled at high confidence as MAX structures (TM-pred score > 0.6). ...
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... BCG, one of the anionic dyes, is generally used as a pH indicator in applications such as growth media for microorganisms and titrations. Because in aqueous solution, at low pH, BCG ionizes and gives a monoanionic form (yellow), while at high pH it becomes blue by giving dianionic form [8]. BCG has several applications in the medical field, including the measurement of serum albumin in blood tests and the detection of protein in urine samples. ...
... Despite the advantage associated with droplet vitrification, effective vitrification is still dependent on extended incubation times in PVS2 that could lead to phytotoxicity (Volk et al., 2013;Nadarajan and Pritchard, 2014). The application of vacuum infiltration vitrification (VIV) is postulated to eliminate the pressure differential of the air spaces found in live plant tissue, and facilitate a 10-fold reduction in PVS2 exposure time as reported for Arabidopsis thaliana, Carica papaya, Passiflora edulis and Laurus nobilis embryos (Nadarajan and Pritchard, 2014;Lukic et al., 2022). In our previous study, it was found that combining the droplet technique with VIV i.e., DVIV ...
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... 8. Certain plant species may expand into new habitats as minimum temperatures rise (Bradley, Wilcove, and Oppenheimer 2010). Elevated minimum temperatures can also slightly increase plant metabolic rates, benefiting processes like nutrient uptake and photosynthesis when they stay within the plant's optimal range (Hussain et al. 2019;Whelehan et al. 2022). 9. ...
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... 63 The form of SPI is similar to the definition of hydrophobicity index. 143 We further investigated the distribution of ΔG ‡ values versus SPI for C10 and C12 substrates combined with different enzyme variants. The distribution conforms to a two-segment, piecewise linear correlation plot with a volcano shape (Figure 5d). ...
... According to current mutation understanding, the aggregation process in proteins is influenced by three crucial residues, namely F15, H18, and F23. [30] Impressively, histidine is the key factor in hIAPP aggregation. ...
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