bluuebunny/crossref_metadata_2025 huggingface dataset:
Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment
Authors: Barkley Dalia , Moncada Reuben , Pour Maayan , Liberman Deborah A. , Dryg Ian , Werba Gregor , Wang Wei , Baron Maayan , Rao Anjali , Xia Bo , França Gustavo S. , Weil Alejandro , Delair Deborah F. , Hajdu Cristina , Lund Amanda W. , Osman Iman , Yanai Itai
Published: December 2021

While genetic tumor heterogeneity has long been recognized, recent work has revealed significant variation among cancer cells at the epigenetic and transcriptional levels. Profiling tumors at the single-cell level in individual cancer types has shown that transcriptional heterogeneity is organized into cancer cell states, implying that diverse cell states may represent stable and functional units with complementary roles in tumor maintenance and progression. However, it remains unclear to what extent these states span tumor types, constituting general features of cancer. Furthermore, the role of cancer cell states in tumor progression and their specific interactions with cells of the tumor microenvironment remain to be elucidated. Here, we perform a pan-cancer single-cell RNA-Seq analysis across 15 cancer types and identify a catalog of 16 gene modules whose expression defines recurrent cancer cell states, including ‘stress’, ‘interferon response’, ‘epithelial-mesenchymal transition’, ‘metal response’, ‘basal’ and ‘ciliated’. Using mouse models, we find that induction of the interferon response module varies by tumor location and is diminished upon elimination of lymphocytes. Moreover, spatial transcriptomic analysis further links the interferon response in cancer cells to T cells and macrophages in the tumor microenvironment. Our work provides a framework for studying how cancer cell states interact with the tumor microenvironment to form organized systems capable of immune evasion, drug resistance, and metastasis.
Light-induced Patterning of Electroactive Bacterial Biofilms
Authors: Zhao Fengjie , Chavez Marko S. , Naughton Kyle L. , Cole Christina M. , Gralnick Jeffrey A. , El-Naggar Mohamed Y. , Boedicker James Q.
Published: December 2021

Electroactive bacterial biofilms can function as living biomaterials that merge the functionality of living cells with electronic components. However, the development of such advanced living electronics has been challenged by the inability to control the geometry of electroactive biofilms relative to solid-state electrodes. Here, we developed a lithographic strategy to pattern conductive biofilms of Shewanella oneidensis by controlling aggregation protein CdrAB expression with a blue light-induced genetic circuit. This controlled deposition enabled S. oneiensis biofilm patterning on transparent electrode surfaces and measurements demonstrated tunable biofilm conduction dependent on pattern size. Controlling biofilm geometry also enabled us, for the first time, to quantify the intrinsic conductivity of living S. oneidensis biofilms and experimentally confirm predictions based on simulations of a recently proposed collision-exchange electron transport mechanism. Overall, we developed a facile technique for controlling electroactive biofilm formation on electrodes, with implications for both studying and harnessing bioelectronics.
A role for CD4 helper cells in HIV control and progression
Authors: Rouzine Igor M.
Published: December 2021

It remains unclear why HIV persists in most untreated individuals, and why a small minority of individuals can control the virus, either spontaneously or after an early treatment. The present work motivated by the striking differences in the functional avidity of CD4 T cells discovered between patient cohorts in a recent study [1] offers an experimentally–testable mathematical model that explains the diverse outcome of infection. The model predicts an arms race between viral dissemination and the proliferation of HIV-specific CD4 helper cells leading to one of two states: a low-viremia state or a high-viremia state. Helper CD4 cells with a higher avidity favor virus control. The parameter segregating spontaneous and post-treatment controllers is the infectivity asymmetry between activated and resting CD4 T cells. The predictions are found to be consistent with the data from [1] and with data on the avidity CD8 T cells [2]. I also analyze the alternative explanation of T cell exhaustion previously proposed to explain the diverse patient cohorts and demonstrate that it does not explain these and some other experimental data.

Importance

Why HIV persists in most untreated individuals, and why a minority can control the virus, either spontaneously or after short treatment, remains unknown. The present study offers a mathematical model of the immune response that explains the differences between the patient cohorts as a result of the arms race between viral dissemination and the proliferation of HIV-specific CD4 T cells. It offers testable predictions and personalized adjustment of early ART to a patient.
Transmission dynamics and control of Sporotrichosis in domestic felines
Authors: Araújo Aurélio A , Codeço Cláudia , Freitas Dayvison F S , de Macedo Priscila M , Pereira Sandro A , Gremião Isabella D F , Coelho Flávio C.
Published: December 2021

Sporotrichosis is a subcutaneous mycosis with a global distribution, also known as “rose gardener’s disease”. Brazil is experiencing a rapid spread of the zoonotic transmission of of Sporothrix brasiliensis, the main etiological agent of this disease in this country, affecting domestic felines. Cost-effective interventions need to be developed to control this emergent public health problem. To allow for the comparison of alternative control strategies, we propose in this paper, a mathematical model representing the transmission of S. brasiliensis among cats, stratified by age and sex. Analytical properties of the model are derived and simulations show possible strategies for reducing the endemic levels of the disease in the cat population, with a positive impact on human health. The scenarios included mass treatment of infected cats and mass implementation of contact reduction practices, such as neutering. The results indicate that mass treatment can reduce substantially the disease prevalence, and this effect is potentialized when combined with neutering or other contact-reduction interventions. On the other hand, contact-reduction methods alone are not sufficient to reduce prevalence.

Author summary

Sporotrichosis, as a neglected tropical mycosis, has in domestic cats a very important reservoir for Sporothrix sp., its pathogen. Infected cats can easily transmit the fungus to other cats and also to humans by means of scratching and biting.

Here we propose a mathematical model incorporating all forms of transmission of Sporothrix within a cat population, taking into account age and sex-related behavioral differences which can affect the transmission dynamics.

The model also includes a treated compartment, which facilitates the exploration of pharmacological interventions to reduce the prevalence of the disease. We derive the next-generation matrix for the model, which allows the calculation of the disease’s basic reproduction number under different scenarios.

Using the model, we explore different control scenarios involving treatment of the disease, but also the contribution of neutering of cats to the reduction of transmission through changes induced by neutering, of the cat’s social interactions.
Control-based continuation: a new approach to prototype synthetic gene networks
Authors: de Cesare Irene , Salzano Davide , di Bernardo Mario , Renson Ludovic , Marucci Lucia
Published: December 2021

Control-Based Continuation (CBC) is a general and systematic method to carry out the bifurcation analysis of physical experiments. CBC does not rely on a mathematical model and thus overcomes the uncertainty introduced when identifying bifurcation curves indirectly through modelling and parameter estimation. We demonstrate, in silico, CBC applicability to biochemical processes by tracking the equilibrium curve of a toggle switch which includes additive process noise and exhibits bistability. We compare results obtained when CBC uses a model-free and model-based control strategy and show that both can track stable and unstable solutions, revealing bistability. We then demonstrate CBC in conditions more representative of a real experiment using an agent-based simulator describing cells growth and division, cell-to-cell variability, spatial distribution, and diffusion of chemicals. We further show how the identified curves can be used for parameter estimation and discuss how CBC can significantly accelerate the prototyping of synthetic gene regulatory networks.
The origin and evolution of loqs2: a gene encoding an antiviral dsRNA binding protein in Aedes mosquitoes
Authors: Estevez-Castro Carlos F. , Rodrigues Murillo F. , Babarit Antinéa , Ferreira Flávia Viana , Marois Eric , Cogni Rodrigo , Marques João Trindade , Olmo Roenick Proveti
Published: December 2021

Mosquito borne viruses such as dengue, Zika, yellow fever and Chikungunya cause millions of infections every year. These viruses are mostly transmitted by two urban-adapted mosquito species, Aedes aegypti and Aedes albopictus, that appear to be more permissive to arbovirus infections compared to closely related species, although mechanistic understanding remains unknown. Aedes mosquitoes may have evolved specialized antiviral mechanisms that potentially contribute to the low impact of viral infection. Recently, we reported the identification of an Aedes specific double-stranded RNA binding protein (dsRBP), named Loqs2, that is involved in the control of infection by dengue and Zika viruses in Ae. aegypti. Loqs2 interacts with two important co-factors of the RNA interference (RNAi) pathway, Loquacious (Loqs) and R2D2, and seems to be a strong regulator of the antiviral defense. However, the origin and evolution of loqs2 remains unclear. Here, we describe that loqs2 likely originated from two independent duplications of the first dsRNA binding domain (dsRBD) of loquacious that occurred before the radiation of the Aedes Stegomyia subgenus. After its origin, our analyses suggest that loqs2 evolved by relaxed positive selection towards neofunctionalization. In fact, loqs2 is evolving at a faster pace compared to other RNAi components such as loquacious, r2d2 and Dicer-2 in Aedes mosquitoes. Unlike loquacious, transcriptomic analysis showed that loqs2 expression is tightly regulated, almost restricted to reproductive tissues in Ae. aegypti and Ae. albopictus. Transgenic mosquitoes engineered to ubiquitously express loqs2 show massive dysregulation of stress response genes and undergo developmental arrest at larval stages. Overall, our results uncover the possible origin and neofunctionalization of a novel antiviral gene, loqs2, in Aedes mosquitoes that ultimately may contribute to their effectiveness as vectors for arboviruses.
Molecular features underlying Pseudomonas aeruginosa persistence in human plasma
Authors: Janet-Maitre Manon , Pont Stéphane , Masson Frerich , Sleiman Serena , Trouillon Julian , Robert-Genthon Mylène , Gallet Benoît , Dumestre-Perard Chantal , Elsen Sylvie , Moriscot Christine , Bardoel Bart , Rooijakkers Suzan , Cretin François , Attrée Ina
Published: December 2021

Pseudomonas aeruginosa, an opportunistic Gram-negative pathogen, is a leading cause of bacteremia with a high mortality rate. We recently reported that P. aeruginosa forms a persister-like sub-population of evaders in human plasma and blood. However, the molecular mechanisms underlying the formation of evaders remained unknown. Here, using a gain-of-function genetic screen, we examined the molecular determinants of P. aeruginosa persistence in plasma. We found that, among other factors, ATP and biotin availability greatly influence bacterial survival in plasma; mutants in pur and bio genes display higher tolerance and persistence, respectively. Electron microscopy combined with energy-dispersive X-ray spectroscopy (EDX) revealed the formation of polyphosphate granules upon incubation in plasma in several clinical strains, implying the bacterial response to a low-energy stress signal. Indeed, mutants with transposon insertions in ppk genes were eliminated in the plasma. Analysis of several steps of the complement cascade and exposure to an outer-membrane-impermeable drug, nisin, suggested that the mutants impede membrane attack complex (MAC) activity per se. Through this study, we shed light on P. aeruginosa response to the plasma conditions and discovered the multifactorial origin of bacterial resilience to MAC that provides a comprehensive picture of the complex interplay between P. aeruginosa and the human complement system.

Author summary

Persistence of bacterial pathogens is a main cause of treatment failure and establishment of chronic bacterial infection. Despite innate immune responses, some bacteria may persist in human blood and plasma. Here we used a genome-wide screen to investigate the molecular determinants influencing Pseudomonas aeruginosa persistence in human plasma facing the complement system. Alongside a multifactorial strategy, we found intracellular levels of ATP and biotin to significantly influence bacterial capacity to deal with membrane attack complex (MAC)-dependent killing. These results underline the need to understand the complex interplay between bacterial pathogens and the human immune system when seeking to develop efficient antibacterial strategies.
Popeye Domain-Containing Protein 1 Scaffolds a Complex of Adenylyl Cyclase 9 and the Two-Pore-Domain Potassium Channel TREK-1 in Heart
Authors: Baldwin Tanya A. , Li Yong , Marsden Autumn , Schindler Roland F.R. , Zhang Musi , Carbajal Anibal Garza , Garcia Mia A. , Venna Venugopal Reddy , Brand Thomas , Dessauer Carmen W.
Published: December 2021

The establishment of macromolecular complexes by scaffolding proteins such as A-kinase anchoring proteins is key to the local production of cAMP by anchored adenylyl cyclase (AC) and the subsequent cAMP signaling necessary for many cardiac functions. We have identified herein a novel AC scaffold, the Popeye domain-containing (POPDC) protein. Unlike other AC scaffolding proteins, POPDC1 binds cAMP with high affinity. The POPDC family of proteins are important for cardiac pacemaking and conduction, due in part to their cAMP-dependent binding and regulation of TREK-1 potassium channels. TREK-1 binds the AC9:POPDC1 complex and co-purifies in a POPDC1-dependent manner with AC9-associated activity in heart. Although the interaction of AC9 and POPDC1 is cAMP independent, TREK-1 association with AC9 and POPDC1 is reduced in an isoproterenol-dependent manner, requiring an intact cAMP binding Popeye domain and AC activity within the complex. We show that deletion of Adcy9 (AC9) gives rise to bradycardia at rest and stress-induced heart rate variability. The phenotype for deletion of Adcy9 is milder than previously observed upon loss of Popdc1, but similar to loss of Kcnk2 (TREK-1). Thus, POPDC1 represents a novel scaffolding protein for AC9 to regulate heart rate control.

ONE-SENTENCE SUMMARY

Adenylyl cyclase type 9 binds in an isoproterenol-dependent manner to the POPDC1:TREK-1 complex regulating heart rate.
HSP70-binding motifs function as protein quality control degrons
Authors: Abildgaard Amanda B. , Voutsinos Vasileios , Petersen Søren D. , Larsen Fia B. , Kampmeyer Caroline , Johansson Kristoffer E. , Stein Amelie , Ravid Tommer , Andréasson Claes , Jensen Michael K. , Lindorff-Larsen Kresten , Hartmann-Petersen Rasmus
Published: December 2021

Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are hydrophobic and rarely contain negatively charged residues, features which are shared with chaperone-binding regions. Here we explore the notion that chaperone-binding regions may function as PQC degrons. When directly tested, we found that a canonical Hsp70-binding motif (the APPY peptide) functioned as a dose-dependent PQC degron both in yeast and in human cells. In yeast, Hsp70, Hsp110, Fes1, and the E3 Ubr1 target the APPY degron. Screening revealed that the sequence space within the chaperone-binding region of APPY that is compatible with degron function is vast. We find that the number of exposed Hsp70-binding sites in the yeast proteome correlates with a reduced protein abundance and half-life. Our results suggest that when protein folding fails, chaperone-binding sites may operate as PQC degrons, and PQC-linked degradation therefore overlaps in specificity with chaperone binding. This sheds new light on how the PQC system has evolved to exploit the intrinsic capacity of chaperones to recognize misfolded proteins, thereby placing them at the nexus of protein folding and degradation.

Significance Statement

It is broadly accepted that misfolded proteins are often rapidly degraded by the ubiquitin-proteasome system, but how cells specifically recognize this immensely diverse group of proteins is largely unknown. Here we show that upon uncoupling of protein folding from protein degradation, a canonical chaperone-binding motif doubles as a degradation signal (degron), and that within the context of a Hsp70-binding region, many sequences are compatible with degron function. We find that degradation is correlated with the number of Hsp70-binding sites within a protein, and that the number of exposed Hsp70-binding sites in the yeast proteome correlates with more rapid degradation.
Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX
Authors: Pan Dongqing , Oyama Ryo , Sato Tomomi , Nakane Takanori , Mizunuma Ryo , Matsuoka Keita , Joti Yasumasa , Tono Kensuke , Nango Eriko , Iwata So , Nakatsu Toru , Kato Hiroaki
Published: December 2021

CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open–close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 monoacylglycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hydroxypropyl methylcellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.
Crystallization and low-resolution structure solution of the SALM3–PTPσ synaptic adhesion complex
Authors: Karki Sudeep , Kajander Tommi
Published: December 2021

Synaptic adhesion molecules are major organizers of the neuronal network and play a crucial role in the regulation of synapse development and maintenance in the brain. Synaptic adhesion-like molecules (SALMs) and leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-PTPs) are adhesion protein families with established synaptic function. Dysfunction of several synaptic adhesion molecules has been linked to cognitive disorders such as autism spectrum disorders and schizophrenia. A recent study of the binding and complex structure of SALM3 and PTPσ using small-angle X-ray scattering revealed a 2:2 complex similar to that observed for the interaction of human SALM5 and PTPδ. However, the molecular structure of the SALM3–PTPσ complex remains to be determined beyond the small-angle X-ray scattering model. Here, the expression, purification, crystallization and initial 6.5 Å resolution structure of the mouse SALM3–PTPσ complex are reported, which further verifies the formation of a 2:2 trans-heterotetrameric complex similar to the crystal structure of human SALM5–PTPδ and validates the architecture of the previously reported small-angle scattering-based solution structure of the SALM3–PTPσ complex. Details of the protein expression and purification, crystal optimization trials, and the initial structure solution and data analysis are provided.
X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure
Authors: Gomez Barroso Juan Arturo , Miranda Mariana Reneé , Pereira Claudio Alejandro , Garratt Richard Charles , Aguilar Carlos Fernando
Published: December 2021

Trypanosoma cruzi is a flagellated protozoan parasite that causes Chagas disease, which represents a serious health problem in the Americas. Nucleoside diphosphate kinases (NDPKs) are key enzymes that are implicated in cellular energy management. TcNDPK1 is the canonical isoform in the T. cruzi parasite. TcNDPK1 has a cytosolic, perinuclear and nuclear distribution. It is also found in non-membrane-bound filaments adjacent to the nucleus. In the present work, X-ray diffraction and in vivo studies of TcNDPK1 are described. The structure reveals a novel, multi-hexameric, left-handed helical oligomer structure. The results of directed mutagenesis studies led to the conclusion that the microscopic TcNDPK1 granules observed in vivo in T. cruzi parasites are made up by the association of TcNDPK1 oligomers. In the absence of experimental data, analysis of the interactions in the X-ray structure of the TcNDPK1 oligomer suggests the probable assembly and disassembly steps: dimerization, assembly of the hexamer as a trimer of dimers, hexamer association to generate the left-handed helical oligomer structure and finally oligomer association in a parallel manner to form the microscopic TcNDPK1 filaments that are observed in vivo in T. cruzi parasites. Oligomer disassembly takes place on the binding of substrate in the active site of TcNDPK1, leading to dissociation of the hexamers. This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1.
Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts
Authors: Axford Danny , Judge Peter J. , Bada Juarez Juan F. , Kwan Tristan O. C. , Birch James , Vinals Javier , Watts Anthony , Moraes Isabel
Published: December 2021

Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photoreceptor and room-temperature diffraction data were acquired. By using transparent and opaque polymer films, two structures, one corresponding to the desensitized, dark-adapted (DA) state and the other to the ground or light-adapted (LA) state, were solved to better than 1.9 Å resolution. All of the key structural features of AR3 were resolved, including the retinal chromophore, which is present as the 13-cis isomer in the DA state and as the all-trans isomer in the LA state. The film-sandwich sample environment enables diffraction data to be recorded at room temperature in both illuminated and dark conditions, which more closely approximate those in vivo. This simple approach is applicable to a wide range of membrane proteins crystallized in LCP and light-sensitive samples in general at synchrotron and laboratory X-ray sources.
Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA
Authors: Petit Guillaume A. , Mohanty Biswaranjan , McMahon Róisín M. , Nebl Stefan , Hilko David H. , Wilde Karyn L. , Scanlon Martin J. , Martin Jennifer L. , Halili Maria A.
Published: December 2021

Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. The crystal structures of oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 show that both fragments bind to a hydrophobic pocket that is formed by a change in the side-chain orientation of Tyr110. This conformational change opens a `cryptic' pocket that is not evident in the apoprotein structure. This binding location was supported by 2D-NMR studies, which identified a chemical shift perturbation of the Tyr110 backbone amide resonance of more than 0.05 p.p.m. upon the addition of 2 mM fragment 1 and of more than 0.04 p.p.m. upon the addition of 1 mM fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (K
d) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the crystal structure models, which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have a high energetic binding affinity due to their relatively small surface area and the few functional groups that are available for intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. The identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.
Best practices for time-resolved serial synchrotron crystallography
Authors: Schulz Eike C. , Yorke Briony A. , Pearson Arwen R. , Mehrabi Pedram
Published: December 2021

With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering
Authors: Kim Jiheon , Pham Ha , Baek Yeongjin , Jo Inseong , Kim Yong-Hak , Ha Nam-Chul
Published: December 2021

The YxaL protein was isolated from the soil bacterium Bacillus velezensis and has been shown to promote the root growth of symbiotic plants. YxaL has further been suggested to act as an exogenous signaling protein to induce the growth and branching of plant roots. Amino acid sequence analysis predicted YxaL to exhibit an eight-bladed β-propeller fold stabilized by six tryptophan-docking motifs and two modified motifs. Protein engineering to improve its structural stability is needed to increase the utility of YxaL as a plant growth-promoting factor. Here, the crystal structure of YxaL from B. velezensis was determined at 1.8 Å resolution to explore its structural features for structure-based protein engineering. The structure showed the typical eight-bladed β-propeller fold with structural variations in the third and fourth blades, which may decrease the stability of the β-propeller fold. Engineered proteins targeting the modified motifs were subsequently created. Crystal structures of the engineered YxaL proteins showed that the typical tryptophan-docking interaction was restored in the third and fourth blades, with increased structural stability, resulting in improved root growth-promoting activity in Arabidopsis seeds. The work is an example of structure-based protein engineering to improve the structural stability of β-propellor fold proteins.
Catalytically active holoHomo sapiensadenosine deaminase I adopts a closed conformation
Authors: Ma Minh Thu , Jennings Maria Rain , Blazeck John , Lieberman Raquel L.
Published: December 2021

Homo sapiensadenosine deaminase 1 (HsADA1; UniProt P00813) is an immunologically relevant enzyme with roles in T-cell activation and modulation of adenosine metabolism and signaling. Patients with genetic deficiency in HsADA1 suffer from severe combined immunodeficiency, and HsADA1 is a therapeutic target in hairy cell leukemias. Historically, insights into the catalytic mechanism and the structural attributes of HsADA1 have been derived from studies of its homologs fromBos taurus(BtADA) andMus musculus(MmADA). Here, the structure of holo HsADA1 is presented, as well as biochemical characterization that confirms its high activity and shows that it is active across a broad pH range. Structurally, holo HsADA1 adopts a closed conformation distinct from the open conformation of holo BtADA. Comparison of holo HsADA1 and MmADA reveals that MmADA also adopts a closed conformation. These findings challenge previous assumptions gleaned from BtADA regarding the conformation of HsADA1 that may be relevant to its immunological interactions, particularly its ability to bind adenosine receptors. From a broader perspective, the structural analysis of HsADA1 presents a cautionary tale for reliance on homologs to make structural inferences relevant to applications such as protein engineering or drug development.
Implications of AlphaFold2 for crystallographic phasing by molecular replacement
Authors: McCoy Airlie J. , Sammito Massimo D. , Read Randy J.
Published: December 2021

The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models.
CryoEM analysis of small plant biocatalysts at sub-2 Å resolution
Authors: Dimos Nicole , Helmer Carl P. O. , Chánique Andrea M. , Wahl Markus C. , Kourist Robert , Hilal Tarek , Loll Bernhard
Published: December 2021

Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial in order to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryoEM) has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes has so far been largely unexplored. Here, it is shown that cryoEM can reveal the structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution, paving the way for the rapid development of new biocatalysts that can provide access to bioactive terpenes and terpenoids.
Understanding reporting boundaries in annual reports: a conceptual framework
Authors: Bayne Lyndie
Published: December 2021

Purpose

The purpose of this paper is to enhance conceptual understanding of reporting boundaries in corporate annual reports by developing a conceptual framework of the rules and principles, referred to here as dimensions, underlying boundaries. A total of nine contemporary regulations/guidelines are compared in terms of the boundary dimensions identified to illustrate similarities and differences in boundary concepts.

Design/methodology/approach

To develop a conceptual framework of reporting boundary dimensions, academic and industry literature were analysed to identify boundary dimensions. Thereafter, nine contemporary regulations/guidelines were compared in terms of these dimensions. A qualitative approach was taken including document analysis and content analysis.

Findings

A total of 10 key boundary dimensions were identified through analysis of academic and industry literature. Each dimension represents a continuum along which regulations/guidelines can position themselves. Taken together, the 10 dimensions provide a comprehensive description of the chosen boundary concept.

Originality/value

The paper contributes to accounting theory by providing a holistic conceptual framework of dimensions relating to reporting boundaries, thus answering calls for more conceptual development of the boundary construct. The conceptual framework and comparison of contemporary regulations/guidelines adds to scarce literature considering financial and non-financial boundaries simultaneously, which is relevant for annual reports. From a practical perspective, the paper brings renewed visibility to boundaries with implications for preparers, users, standard setters and auditors of annual reports.
Parametric and V&V study in a fundamental CFD process: revisiting the lid-driven cavity flow
Authors: Ge Mingming , Zhang Xin-Lei , Brookshire Kaleb , Coutier-Delgosha Olivier
Published: December 2021

Purpose

The openings on aircraft structures can be modeled from an aerodynamical point of view as lid-driven cavities (LDC). This paper aims to show the primary verification and validation (V&V) process in computational fluid dynamics (CFD, and to investigate the influences of numerical settings on the efficiency and accuracy for solving the LDC problem.

Design/methodology/approach

To dig into the details of CFD approaches, this paper outlines the design, implementation, V&V and results of an efficient explicit algorithm. The parametric study is performed thoroughly focusing on various iteration methods, grid density discretization terms and Reynolds number effects.

Findings

This study parameterized the numerical implementation which provides empirical insights into how computational accuracy and efficiency are affected by changing numerical settings. At a low Reynolds number (not over 1,000), the time-derivative preconditioning is necessary, and k = 0.1 can be the optimal value to guarantee the efficiency, as well as the stability. A larger artificial viscosity (c = 1/16) would relieve the calculating oscillation issue but proportionally increase the discretization error. Furthermore, the iteration method and the mesh quality are two key factors that affect the convergence efficiency, thus need to be selected “wisely”.

Practical implications

The study shows how numerical implementation can enhance an accurate and efficient solution. This workflow can be used to determine the best parameter settings whenever CFD researchers applying this LDC problem as a complementary design tool for testing newly developed solvers.

Originality/value

The studied LDC problem is representative of CFD analysis in real aircraft structures. These numerical simulations provide a cost-effective and convenient tool to understand the parameter sensitivity, solution receptivity and physics of the CFD process.
The correlates of energy management practices and sales performance of small family food firms in Turkey
Authors: Onjewu Adah-Kole Emmanuel , Puntaier Elmar , Hussain Sundas
Published: December 2021

Purpose

While pursuing energy management, firms simultaneously strive to boost sales as a path towards economic performance. Also, the literature suggests that family firms exhibit greater environmental commitment than their non-family counterparts. To examine these contentions, this review espouses contingency theory to interrogate the correlations of (1) energy consumption targets, (2) energy efficiency enhancing measures, (3) energy consumption monitoring and (4) the domestic sales performance of small family firms in Turkey's food sector.

Design/methodology/approach

Data were sourced from the World Bank Enterprise Survey. A sample of 137 family firms in food production, processing and retail was analysed using non-linear structural equation modelling. Path coefficients were determined to estimate the extent to which energy management practices predict domestic sales.

Findings

The path analysis revealed that although energy consumption targets do not directly increase sales performance, they stimulate firms' energy efficiency enhancement measures and energy consumption monitoring to produce this effect by 21%.

Research limitations/implications

The contingency lens espoused leaves room to capture further antecedents in small family food firms' technical, managerial, ownership, operational and architectural configuration that may also interact with or predict the propensity for energy management.

Practical implications

For practitioners, the inherent findings demonstrate that there are firm-specific material benefits arising from adopting energy management practices. And, although small firms such as family food businesses may have low energy intensities, they can improve their sales performance by setting energy targets, installing energy efficiency enhancing measures and embarking on energy consumption monitoring.

Social implications

Public stakeholders in Turkey such as the Ministry of Energy and Natural Resources, the General Directorate of Energy Affairs and affiliate institutions can reflect on these findings to develop a coherent national energy management policy for small firms. Such initiatives are especially relevant to Turkey and its ambitions to join the EU which requires member states to set up a national energy efficiency action plan.

Originality/value

This inquiry is one of the first to examine energy management in the food sector at the family firm level through the contingency lens. Theoretically, the results draw attention and shed new light on disparate energy management practices and their discrete yet substantial contribution to sales performance.
An innovative deterministic algorithm for optimal placement of micro phasor measurement units in radial electricity distribution systems
Authors: Gholizadeh Manghutay Aref , Salay Naderi Mehdi , Fathi Seyed Hamid
Published: December 2021

Purpose

Heuristic algorithms have been widely used in different types of optimization problems. Their unique features in terms of running time and flexibility have made them superior to deterministic algorithms. To accurately compare different heuristic algorithms in solving optimization problems, the final optimal solution needs to be known. Existing deterministic methods such as Exhaustive Search and Integer Linear Programming can provide the final global optimal solution for small-scale optimization problems. However, as the system grows the number of calculations and required memory size incredibly increases, so applying existing deterministic methods is no longer possible for medium and large-scale systems. The purpose of this paper is to introduce a novel deterministic method with short running time and small memory size requirement for optimal placement of Micro Phasor Measurement Units (µPMUs) in radial electricity distribution systems to make the system completely observable.

Design/methodology/approach

First, the principle of the method is explained and the observability of the system is analyzed. Then, the algorithm’s running time and memory usage when applying on some of the modified versions of the Institute of Electrical and Electronics Engineers 123-node test feeder are obtained and compared with those of its deterministic counterparts.

Findings

Because of the innovative method of step-by-step placement of µPMUs, a unique method is developed. Simulation results elucidate that the proposed method has unique features of short running time and small memory size requirements.

Originality/value

While the mathematical background of the observability study of electricity distribution systems is very well-presented in the referenced papers, the proposed step-by-step placement method of µPMUs, which shrinks unobservable parts of the system in each step, is not discussed yet. The presented paper is directly applicable to typical problems in the field of power systems.
Sustainable business models to create sustainable competitive advantages: strategic approach to overcoming COVID-19 crisis and improve financial performance
Authors: Mattera Marina , Alba Ruiz-Morales Carmen , Gava Luana , Soto Federico
Published: December 2021

Purpose

The purpose of this study is to evaluate whether the implementation of sustainable business models contributes to improving a firm’s performance during a global crisis, such as the one caused by COVID-19. Based on the triple bottom line theory, the paper explores the relation between the creation of value through solid corporate social responsibility (CSR) strategies, United Nations (UN) Global Compact’s (GC) business model proposals and Global Reporting Initiative’s (GRI) reporting scheme.

Design/methodology/approach

The present paper studies companies within the European Union, focusing specifically on the long-term impact of using the world’s most widely used standards for sustainability reporting – the GRI’s standards and/or the UNGC management models, as well as on the firm’s performance based on the financial results during COVID-19 crisis. To achieve this goal, the study analyses the share price of firms publicly listed in the FTSEMIB (benchmark index of Italy’s largest trading platform) out of those companies that are implementing the UN and GRI’s tools.

Findings

Findings show how a commitment to sustainable business models and long-term CSR strategies can contribute to firm’s ability to overcome periods of economic crisis. Furthermore, implementing GRI standards and UNGC guidelines within the business model seems to have a positive impact in overcoming a hard context such as COVID-19. In addition, it contributes to a better understanding of stakeholders’ needs, consumer profiling and value creation.

Originality/value

This study evaluates firms’ business models, considering the effects of decisions made in the context of COVID-19. The role of UNGC and GRI is evaluated in terms of their contribution to firms’ financial performance and corporate reputation during a context of hardship. Consequently, this study contributes to academia and practice, adding value in areas related to strategic planning and business model design.
The strategic innovation under information technological turbulence: the role of organisational resilience in competitive advantage
Authors: Pratono Aluisius Hery
Published: December 2021

Purpose

This study aims to propose a structural model drawing from the theoretical literature, extending the relative research fields to the competitive strategy. The empirical results involve data collection of 582 data that represents various enterprises in the Indonesian context. The authors develop four scenarios of strategic innovation based on the empirical findings, which extend the discussion on the concept of competitive strategy.

Design/methodology/approach

This paper aims to examine the impact of organisational resilience and marketing communication on competitive advantage through new product development under information technological turbulence.

Findings

The results indicate that product development is less effective to firm competitive advantage during the high information technological turbulence than during low information technological turbulence. This study shows that organisational resilience and marketing communication help firms achieve a competitive advantage. The authors also identify four scenarios for strategic innovation, drawing from empirical results.

Originality/value

This paper extends the literature of resource-based views by proposing a model that concerns product development as the primary determinant of competitive advantage. In addition, this study discusses the intersection between the concept of dynamic capability and contingency theory by examining how firms deal with information technological turbulence.