bluuebunny/crossref_metadata_2025 huggingface dataset:
Interleukin‐1β activated c‐FOS transcription factor binds preferentially to a specific allele of the matrix metalloproteinase‐13 promoter and increases susceptibility to endometriosis
Authors: Pandit Anuradha , Das Mahapatra Pramathes , Saha Priyanka , Srivastava Amit Kumar , Swarnakar Snehasikta
Published: May 2022

Endometriosis is a benign gynecological condition characterized by increased growth, inflammation, invasion, and angiogenesis, partly regulated by a class of enzymes called matrix metalloproteinases (MMPs). The importance of a few MMPs, e.g., MMP‐9, ‐3, and ‐7 has been studied in endometriosis progression. Although MMP‐13 plays an essential role in bone regeneration and cancer, no report has been found on the part of MMP‐13 and endometriosis progression. We found the upregulation of MMP‐13 expression and activity in patients having endometriosis in the eastern Indian population. In addition, the −77A/G polymorphism of the MMP13 promoter (rs: 2252070) is associated with regulating transcription and subsequent susceptibility to disease. In eastern Indian case‐control groups, the effect of the −77A/G single‐nucleotide polymorphism on MMP13 promoter activity and its relationship with endometriosis susceptibility was studied. The AG genotype was shown to be more predisposed to endometriosis risk than the GG genotype (p: 0.02; odds ratio [OR]: 1.65, 95% confidence interval [CI]: 1.10–2.49), also AG genotype was more frequent in late‐stage patients compared to early‐stage (p: 0.03, OR: 2.0, 95% CI: 1.09–3.66). Furthermore, the MMP13 gene levels were greater in AA compared to GG individuals. Additionally, MMP13 promoter‐reporter experiments in cultured endometrial epithelial cells and in silico analyses both demonstrated increased transcriptional activity near the G to A transition under basal/IL‐1β ‐induced/c‐FOS overexpressed condition. Overall, c‐FOS tighter binding to the A allele‐carrying promoter enhances MMP13 transcription, which is further amplified by IL‐1β due to increased c‐FOS phosphorylation, promoting MMP‐13 production and endometriosis risk.
A gain‐of‐function mutation in the ITPR1 gating domain causes male infertility in mice
Authors: Sun Bo , Ni Mingke , Tian Shanshan , Guo Wenting , Cai Shitian , Sondergaard Mads T. , Chen Yongxiang , Mu Yongxin , Estillore John P. , Wang Ruiwu , Chen Ju , Overgaard Michael T. , Fill Michael , Ramos‐Franco Josefina , Nyegaard Mette , Wayne Chen Sui Rong
Published: May 2022

Inositol 1,4,5‐trisphosphate receptor 1 (ITPR1) is an intracellular Ca2+ release channel critical for numerous cellular processes. Despite its ubiquitous physiological significance, ITPR1 mutations have thus far been linked to primarily movement disorders. Surprisingly, most disease‐associated ITPR1 mutations generate a loss of function. This leaves our understanding of ITPR1‐associated pathology oddly one‐sided, as little is known about the pathological consequences of ITPR1 gain of function (GOF). To this end, we generated an ITPR1 gating domain mutation (D2594K) that substantially enhanced the inositol trisphosphate (IP3)‐sensitivity of ITPR1, and a mouse model expressing this ITPR1‐D2594K+/− GOF mutation. We found that heterozygous ITPR1‐D2594K+/− mutant mice exhibited male infertility, azoospermia, and acrosome loss. Furthermore, we functionally characterized a human ITPR1 variant V494I identified in the UK Biobank database as potentially associated with disorders of the testis. We found that the ITPR1‐V494I variant significantly enhanced IP3‐induced Ca2+ release in HEK293 cells. Thus, ITPR1 hyperactivity may increase the risk of testicular dysfunction.
Interaction between mesenchymal stem cells and myoblasts in the context of facioscapulohumeral muscular dystrophy contributes to the disease phenotype
Authors: Kiseleva Ekaterina , Serbina Olesya , Karpukhina Anna , Mouly Vincent , Vassetzky Yegor S.
Published: May 2022

Facioscapulohumeral muscular dystrophy (FSHD) is a genetic disease associated with ectopic expression of the DUX4 gene in skeletal muscle. Muscle degeneration in FSHD is accompanied by muscle tissue replacement with fat and connective tissue. Expression of DUX4 in myoblasts stimulates mesenchymal stem cells (MSC) migration via the CXCR4‐CXCL12 axis. MSCs participate in adipose and connective tissue formation and can contribute to fibrosis. Here we studied the interaction between myoblasts and MSCs and the consequences of this interaction in the FSHD context. We used cell motility assays and coculture of MSCs with myoblasts to study their mutual effects on cell migration, differentiation, proliferation, and extracellular matrix formation. The growth medium conditioned by FSHD myoblasts stimulated MSCs migration 1.6‐fold (p < 0.04) compared to nonconditioned medium. Blocking the CXCL12‐CXCR4 axis with the CXCR4 inhibitor (AMD3100) or neutralizing antibodies to CXCL12 abolished this effect. FSHD myoblasts stimulated MSC proliferation 1.5−2 times (p < 0.05) compared to control myoblasts, while the presence of MSCs impaired myoblast differentiation. Under inflammatory conditions, medium conditioned by FSHD myoblasts stimulated collagen secretion by MSCs 2.2‐fold as compared to the nonconditioned medium, p < 0.03. FSHD myoblasts attract MSCs via the CXCL12‐CXCR4 axis, stimulate MSC proliferation and collagen secretion by MSCs. Interaction between MSCs and FSHD myoblasts accounts for several important aspects of FSHD pathophysiology. The CXCL12‐CXCR4 axis may serve as a potential target to improve the state of the diseased muscles.
Biopolymer magnetic chitosan–graphene oxide composite for removal and extraction of aromatic amines from aqueous samples
Authors: Zeb Muhammad Amir , Shah Jasmin , Jan Muhammad Rasul
Published: May 2022

BACKGROUND

Magnetic chitosan was crosslinked with graphene oxide and a magnetic chitosan–graphene oxide composite was synthesized and characterized. The composite was used for the removal and extraction of aromatic amines like aniline, N,N‐dimethylaniline and N,N‐diethylaniline.

RESULTS

Experimental factors affecting the adsorption process such as solution pH, time of contact, amount of adsorbent, initial concentration of analyte and temperature of solution were studied. The maximum adsorption capacity was found to be 7.55 mg g−1 for aniline, 6.96 mg g−1 for N,N‐dimethylaniline and 6.86 mg g−1 for N,N‐diethylaniline using pH 7 at room temperature. Kinetic and adsorption isotherm models were applied to the data which showed the best fit of experimental data to pseudo‐second‐order kinetic model and Langmuir isotherm for all three analytes.

CONCLUSIONS

The adsorption process was found to be spontaneous and exothermic as revealed by thermodynamic study. The maximum recoveries for aniline, N,N‐dimethylaniline and N,N‐diethylaniline were 98.56%, 97.05% and 95.26%, respectively. Successful application of the adsorbent was found for spiked aqueous samples. © 2022 Society of Chemical Industry (SCI).
Highly restricted SARS-CoV-2 receptor expression and resistance to infection by primary human monocytes and monocyte-derived macrophages
Authors: Zankharia Urvi , Yadav Anjana , Yi Yanjie , Hahn Beatrice H , Collman Ronald G
Published: May 2022

Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV2), which causes the disease COVID-19, has caused an unprecedented global pandemic. Angiotensin-converting enzyme 2 (ACE2) is the major cellular receptor for SARS-CoV2 entry, which is facilitated by viral Spike priming by cellular TMPRSS2. Macrophages play an important role in innate viral defense and are also involved in aberrant immune activation that occurs in COVID-19, and thus direct macrophage infection might contribute to severity of SARS-CoV2 infection. Here, we demonstrate that monocytes and monocyte-derived macrophages (MDM) under in vitro conditions express low-to-undetectable levels of ACE2 and TMPRSS2 and minimal coexpression. Expression of these receptors remained low in MDM induced to different subtypes such as unpolarized, M1 and M2 polarized. Untreated, unpolarized, M1 polarized, and M2 polarized MDM were all resistant to infection with SARS-CoV2 pseudotyped virions. These findings suggest that direct infection of myeloid cells is unlikely to be a major mechanism of SARS-CoV2 pathogenesis.

Summary sentence: Monocytes and macrophages express minimal ACE2 and TMPRSS2 and resist SARS-CoV-2 Spike-mediated infection, suggesting direct myeloid cell infection is unlikely a major contributor to pathogenesis.
Redefining the simplicity of the craniomandibular complex of nightjars: The case of Systellura longirostris (Aves: Caprimulgidae) by means of anatomical network analysis
Authors: De Mendoza Ricardo S. , Carril Julieta , Degrange Federico J. , Demmel Ferreira María M. , Nieto Mauro N. , Tambussi Claudia P.
Published: May 2022

To study morphological evolution, it is necessary to combine information from multiple intersecting research fields. Here, we report on the structure of the bony and muscular elements of the craniomandibular complex of birds, highlighting its morphological architecture and complexity (or simplification) in the context of anatomical networks of the Band‐winged Nightjar Systellura longirostris (Caprimulgiformes, Caprimulgidae). This species has skull osteology and jaw myology that departs from the general structural plan of the craniomandibular complex of Neornithes and is considered morphologically simple. Our goal is to test if its simplification is also reflected in its anatomical network, particularly in those parameters that measure complexity and to explore if the distribution of the networks in a phylomorphospace is conditioned by their evolutionary history or by convergence. Our results show that S. longirostris clusters with other Strisores and momotids and is segregated from the other bird species analyzed when plotted in the phylomorphospace, as a consequence of convergence in the network parameters. Systellura has a craniomandibular complex consisting of fewer muscles connecting more bones than the model species (e.g., the rock pigeon or the guira cuckoo). In this sense, Systellura is actually more complex regarding the number of integrative bony parts, while its craniomandibular complex is simpler. According to its anatomical network, Systellura also can be interpreted as less complex, particularly compared with other Strisores and taxa that reflect the general structure of the craniomandibular complex in Neornithes.
Absence of the Rpb9 subunit of RNA polymerase II reduces the chronological life span in fission yeast
Authors: Bhardwaj Vaibhav , Sharma Nimisha
Published: May 2022

Fission yeast RNA polymerase II consists of 12 subunits, Rpb1‐Rpb12. Among these subunits, Rpb9 is the only subunit whose absence does not cause lethality under optimum growth conditions in fission yeast. However, an rpb9 null fission yeast mutant exhibits a slow‐growth phenotype under optimum growth conditions and a defect in survival under environmental and genotoxic stress conditions. To further gain an understanding of its physiological roles, in the present study we have elucidated the role of the Rpb9 subunit in chronological aging using fission yeast as the model organism. Our results provide evidence that the absence of Rpb9 reduces the chronological life span in fission yeast. Our data further shows that lack of Rpb9 in fission yeast causes oxidative stress sensitivity and accumulation of reactive oxygen species during the stationary phase. Our domain mapping experiments have demonstrated that the Rpb9 region encompassing its amino‐terminal zinc finger domain and the central linker region is important for the role of Rpb9 in chronological aging. Finally, we also show that expression of the budding yeast or human Rpb9 ortholog can functionally complement the reduced chronological life span phenotype of the fission yeast rpb9 deletion mutant. Taken together, our study has identified a new role of the Rpb9 subunit in chronological aging.
A rapid and environmentally friendly method for determination of parabens preservatives in flavors by supercritical fluid chromatography‐tandem mass spectrometry
Authors: Yang Fei , Dong Hao , Zhang Fengmei , Shao Jimin , Wang Ying , Deng Huimin , Tang Gangling , Zhang Xiaotao , Li Bo , Liu Shanshan
Published: May 2022

A rapid method for determination of parabens preservatives (methyl paraben, ethyl paraben, isopropyl paraben, propyl paraben, isobutyl paraben, and butyl paraben) in flavors was established by using supercritical fluid chromatography‐tandem mass spectrometry combined with dispersive solid‐phase extraction. After adding methanol and primary secondary amine to the sample simultaneously, high extraction efficiency and good sample cleanup could be obtained by simple shaking. Parabens were well separated on a Chiralpak IG‐3 column in 6 min by gradient elution. Recoveries from spiked blank samples at 0.5, 1.0, and 5.0 mg/kg were determined to be 88.3–106.6%with relative standard deviations less than 8.0%. All analytes achieved good linear relation (r ≥ 0.999 2). The limits of detection for all analytes ranged from 0.03 to 0.09 mg/kg and the limits of quantification from 0.11 to 0.31 mg/kg, respectively. A total of 20 actual samples were successfully analyzed by taking the proposed method. Being simple, rapid, green, and reliable, this method can be taken for the determination of parabens preservatives in flavors.
Ototoxicity of Long‐Term α‐Difluoromethylornithine for Skin Cancer Prevention
Authors: Chow Cynthia L. , Havighurst Thomas , Lozar Taja , Jones Todd D. , Kim KyungMann , Bailey Howard H.
Published: May 2022

Objective

Evaluate the effects of α‐difluoromethylornithine (DFMO) on hearing thresholds as part of a randomized, double‐blind, placebo‐controlled trial.

Methods

Subjects were randomized and assigned to the control (placebo) or experimental (DFMO) group. DFMO or placebo were administered orally (500 mg/m2/day) for up to 5 years.

Results

Subjects taking DFMO had, on average, increased hearing thresholds from baseline across the frequency range compared to subjects in the control group. Statistical analysis revealed this was significant in the lower frequency range.

Conclusions

This randomized controlled trial revealed the presence of increased hearing thresholds associated with long‐term DFMO use. As a whole, DFMO may help prevent and treat certain types of cancers; however, it can result in some degree of hearing loss even when administered at low doses. This study further highlights the importance of closely monitoring hearing thresholds in subjects taking DFMO. Laryngoscope, 133:676–682, 2023
Tribological performance of protic ionic liquids containing dibutyldithiophosphate as lubricating additives in O/W emulsions
Authors: Ju Chao , Zhao Qin , Wang Xiaobo
Published: May 2022

A series of protic ionic liquids (PILs) containing dibutyldithiophosphate were simply synthesised and used as lubricant additive in base emulsion. The physico‐chemical and lubricating properties of PILs in emulsion were systematically investigated. The stability of prepared emulsions containing PILs were similar with base emulsions by particle size distribution tests. Compared with traditional additive of polysulfide, the PILs in emulsion exhibited superior lubricating properties under harsh conditions. Surprisingly, the oil‐miscible O‐PILs in emulsion showed better friction and wear reduction than water‐miscible T‐PILs in emulsion. The stable protective films formed on the steel surface by results of scanning electron microscope and X‐ray photoelectron spectroscopy were the main reason for the preferable performance.
Experiences and happiness: The role of gender
Authors: Brakus J. Joško , Chen Weifeng , Schmitt Bernd , Zarantonello Lia
Published: May 2022

It is well established that experiences make people happy, but we still know little about how individual differences affect the relationship between consumption of experiences and happiness. This study focuses on gender as the predictor of happiness and addresses the following question: Do women and men differ in the way they attain happiness from consumption of experiences? Considering that research shows that women and men differ in how they process information, it is possible that they differ in how much they reflect on an experience too. Therefore, this study also investigates how the relationship between consumption of experiences and gender is moderated by Need for Cognition (NFC) in affecting subjective happiness. The results of a survey of adult consumers show than women derive more happiness and life satisfaction from meaningful experiences than men whereas men derive more happiness and satisfaction with life from pleasurable experiences than women. NFC moderates these results. The study provides evidence for the distinction between pleasure and meaning in consumption contexts and for the important role of gender in consumption of experiences. Its results imply that design and structuring of commercial experiences should take customer gender into account.
Benzimidazolone‐Dioxazine Pigments‐Based Conjugated Polymers for Organic Field‐Effect Transistor
Authors: Tung Wei‐Yao , Pu Cheng , Huang Yi‐Fan , Xie Wei , Cheng Chung‐Fu , Lai Yun‐Yu , Li Xiang , Lin Heng‐Yi , Lai Yueh‐Ting , Chen Kun , Wang Chien‐Lung , Zhu Yu
Published: May 2022

Molecules based on benzimidazolone‐dioxazine are known as blue/violet pigments and have been commercialized for decades. However, unfavorable solubility limits the application of these structures as building blocks of conjugated polymers despite their low band gaps. Herein, a series of donor–acceptor conjugated polymers containing soluble benzimidazolone‐dioxazine structures as the acceptors and oligothiophene as donors are synthesized and investigated. With increasing numbers of thiophene rings, the steric hindrance diminishes and high molecular weight polymers can be achieved, leading to an improved performance in organic field effect transistor devices. The hole mobility of polymers with three to six thiophene units is in the order of 10−1 cm2 V−1 s −1. Among all the polymers, polymer P3 with three thiophene units between benzimidazolone‐dioxazine structures shows the best hole mobility of 0.4 cm2 V−1 s −1. Grazing‐incidence wide‐angle X‐ray scattering results reveal that the high mobility of organic field‐effect transistors (OFETs) can be accredited by matched donor–acceptor packing in the solid thin films.
Estimating the motor unit number of the flexor carpi ulnaris muscle with MScanFit MUNE
Authors: Alaydin Halil Can , Turkmen Nur , Boran H. Evren , Cengiz Bulent
Published: May 2022

Introduction/Aims

MScanFit motor unit number estimation (MUNE) is a promising method for motor unit estimation and is reported to have good reliability in distal and small muscles. In this study, we investigated the reliability of MScanFit MUNE in a proximal forearm muscle, the flexor carpi ulnaris.

Methods

Twenty healthy volunteers were included in this study, and 15 participants were re‐evaluated in a second session. The ulnar nerve was stimulated at the elbow and a compound muscle action potential (CMAP) scan from the flexor carpi ulnaris (FCU) muscle was recorded from each arm. CMAP, MUNE, and other motor unit parameters were obtained. Reproducibility was evaluated using intraclass correlation coefficients (ICCs).

Results

The average MUNE from 40 FCU muscles was 90.9 (standard deviation: 16.4). MScanFit MUNE and CMAP were not significantly different between the dominant and non‐dominant sides. The ICC indicated good reliability between sessions for each side (0.81 and 0.8, respectively).

Discussion

Our results indicate that MScanFit MUNE is a feasible method with good reproducibility for MUNE of the FCU muscle.
Secondary analysis of a university‐based weight loss program in on‐campus versus off‐campus employees
Authors: Clina Julianne G. , Pan Zhaoxing , Wyatt Holly R. , Peters John C. , Hill James O. , Sayer R. Drew
Published: May 2022

Introduction

Many barriers prevent individuals from regularly engaging in physical activity (PA), including lack of time and access to facilities. Providing free gym membership close to one's work may alleviate both time and financial barriers, increase PA, and result in greater weight loss. The purpose of this secondary analysis was to determine if gym usage, self‐reported leisure PA, and weight loss differed between participants working on the University of Colorado Anschutz Medical Campus (ON) versus working off‐campus (OFF) during a 6‐month weight loss trial.

Methods

117 adults (ON, n = 62; OFF, n = 55) with overweight or obesity received free gym memberships for the duration of trial. Average gym check ins/week, self‐report leisure PA, weight, and fat and lean mass were compared between groups.

Results

ON reported more check‐ins than OFF (ON, 0.93 ± 0.16 times/week; OFF, 0.55 ± 0.10 times/week p = 0.038). Both groups reported increased leisure PA, with ON reporting more leisure PA than OFF at month 4. Both groups had reductions in weight and fat mass, which were similar between groups.

Conclusion

Gym usage in both groups was low, suggesting that convenient and free gym access only marginally promoted use of provided facilities, likely having little additional impact on PA and weight change.

CLINICAL TRIAL REGISTRATION

The parent trial was registered at clinicaltrials.gov: NCT02627105.
Mandatory Schooling of Girls Improved Their Children's Health: Evidence from Turkey's 1997 Education Reform
Authors: Dursun Bahadır , Cesur Resul , Kelly Inas R.
Published: May 2022

This study examines the impact of mandatory maternal education on child health in Turkey, where a non‐trivial fraction of families restricted their daughters’ schooling due to social and cultural barriers. The analysis employs two large data sets and exploits a quasi‐experiment involving an education reform that increased compulsory schooling. Results show that an increase in mother's schooling improves child health at birth (as measured by factors such as low birth weight and premature birth) and lowers child mortality. The current study on the intergenerational benefits of compulsory schooling arguably provides the strongest evidence supporting the argument that mandatory female education has substantial nonpecuniary benefits in terms of the health of the offspring in societies where female education is stigmatized. The implications of this research extend beyond girls’ schooling and suggest that compulsory human capital investments in children can correct market failures when families underinvest in their children because of social or cultural barriers.
Core concepts in pharmacoepidemiology: Fundamentals of the cohort and case–control study designs
Authors: Pottegård Anton
Published: May 2022

In this review paper, I outline the principles of the cohort as a sampling frame and provide a basic introduction to the cohort study design and the case–control study design, two of the most important designs in the pharmacoepidemiologist's toolbox. Further, I discuss when to prefer one design over the other. The paper is intended as a primer for people new to the field of pharmacoepidemiology and contains a range of suggestions for additional reading regarding the study designs and related epidemiological topics.
Reliability analysis for command‐and‐control systems based on edge extension diagram and binary decision diagram
Authors: Li Yifan , Huang Hong‐Zhong , Zhang Tingyu , Huang Sizhe , Li Yahua
Published: May 2022

As the central nervous system of modern information warfare, the command‐and‐control network becomes the brain of command and the strategic target of the enemy's primary attack during the operation. In this paper, a method based on edge extension diagram (EED) and binary decision diagram (BDD) is proposed to evaluate the reliability of connectivity within the basic command post of command‐and‐control network, which is solving the problem that the conventional methods failed to model failure probabilities of node links and with low calculation efficiency. First, graph simplification of network topology, extension of nodes under reliable state, construction of path functions, replacement of associated edges, variable sorting, construction of binary decision graphs, and recursive calculation to evaluate the reliability of the connection between the two ends of the command‐and‐control network. Then, further analyze and sort the variable importance of the command‐and‐control network and analyze the sensitivity of the network topology. This paper contributes to the reliability assessment of command‐and‐control network system, the identification and maintenance of key network nodes, and the design of network topology structure.
The role of cytokines and their antagonists in the treatment of COVID‐19 patients
Authors: Mohseni Afshar Zeinab , Barary Mohammad , Babazadeh Arefeh , Tavakoli Pirzaman Ali , Hosseinzadeh Rezvan , Alijanpour Amirmasoud , Allahgholipour Amirreza , Miri Seyed Rouhollah , Sio Terence T. , Sullman Mark J. M. , Carson‐Chahhoud Kristin , Ebrahimpour Soheil
Published: May 2022

The coronavirus disease 2019 (COVID‐19) has various presentations, of which immune dysregulation or the so‐called cytokine storm syndrome (COVID‐CSS) is prominent. Even though cytokines are vital regulators of body immunoinflammatory responses, their exaggerated release can be harmful. This hyperinflammatory response is more commonly observed during severe COVID‐19 infections, caused by the excessive release of pro‐inflammatory cytokines, such as interleukin‐1 (IL‐1), IL‐6, IL‐8, tumour necrosis factor, granulocyte‐macrophage colony‐stimulating factor, and interferon‐gamma, making their blockers and antagonists of great interest as therapeutic options in this condition. Thus, the pathophysiology of excessive cytokine secretion is outlined, and their most important blockers and antagonists are discussed, mainly focussing on tocilizumab, an interleukin‐6 receptor blocker approved to treat severe COVID‐19 infections.
Biochemical mechanism of phosphorus limitation impairing nitrogen fixation in diazotrophic bacterium Klebsiella variicola W12
Authors: Zhang Li‐Mei , Silvano Eleonora , Rihtman Branko , Aguilo‐Ferretjans Maria , Han Bing , Shi Wei , Chen Yin
Published: May 2022

Introduction

Biological nitrogen (N) fixation (BNF) plays a key role in nitrogen supply in agricultural and natural ecosystems. Harnessing BNF can substantially reduce dependence on chemical fertilizer in agroecosystems and hence can contribute to sustainable agriculture. However, a number of field studies have demonstrated that BNF can be largely suppressed in phosphorus (P)‐deficient environments, while the underlying mechanism is not well understood.

Materials & Methods

In this study, comparative proteomics and lipidomics analyses were conducted on a diazotrophic bacterium Klebsiella variicola W12 under P‐deficient and P‐replete conditions to gain insight into how P availability affects N fixation.

Results

Under P deficiency, N fixation activity of K. variicola W12 was severely repressed. In response to P limitation, the bacterium synthesized P‐free ornithine lipids to replace glycerophospholipids in its membrane to reduce cellular demand for P. Comparative proteomics showed that P limitation resulted in upregulation of the PhoBR two‐component system, a range of organic and inorganic P uptake and transport systems, while nitrogenase and N‐fixation‐related transcriptional regulators NifL and NifA were downregulated.

Conclusion

These results revealed lipid renovation as an adaptation strategy for N2‐fixing microbes to survive under P stress and provided biochemical evidence on how P availability regulates BNF. A conceptual model of N–P coupling at the microbial metabolism level is therefore proposed. Our study provides a simple yet plausible explanation of how P deficiency suppresses BNF observed in the field and highlights the importance of regulating P availability to maximize the potential of BNF in agroecosystems for agriculture sustainable production.
Engineering Functional Membrane–Membrane Interfaces by InterSpy
Authors: Moghimianavval Hossein , Patel Chintan , Mohapatra Sonisilpa , Hwang Sung‐Won , Kayikcioglu Tunc , Bashirzadeh Yashar , Liu Allen P. , Ha Taekjip
Published: May 2022

Engineering synthetic interfaces between membranes has potential applications in designing non‐native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane–membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane–membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell‐free expression (CFE) system. By utilizing co‐translational helix insertion, cell‐free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane–membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity‐inducing proteins. This technology may also prove useful where cell‐cell contacts and communication are recreated in a controlled manner using minimal components.
Organic Small Molecules with Electrochemical‐Active Phenolic Enolate Groups for Ready‐to‐Charge Organic Sodium‐Ion Batteries
Authors: Zhang Hang , Gao Yun , Chen Mingzhe , Li Lin , Li Li , Qiao Yun , Li Weijie , Wang Jiazhao , Chou Shu‐Lei
Published: May 2022

Organic materials have attracted much attention in sodium ion batteries (SIBs) because of their advantages such as being environmentally benign and having high designability. Capacities and cycle life of organic materials are the most important parameters in most research which has been paid much effort to obtain an impressive electrochemical performance on the material level, and the sodium‐detachable ability of these materials to directly match with the sodium‐free anode is neglected. In this work, one organic sodium salt (C6H2Na2O6) exhibits the unique ability (charging first in half cell) unlike other reported organic cathode materials (normally discharging first) for SIBs. The redox mechanism and structure change are investigated by in situ and ex situ tests to give a better understanding for C6H2Na2O6. Satisfying electrochemical performance (74% capacity retention after 600 cycles at 0.05 A g−1 and 63% capacity retention at 5 A g−1 when compared with capacity at 0.05 A g−1) is achieved by the C6H2Na2O6 electrode. In addition, matched with hard carbon, full cells are assembled successfully like other transition metal containing cathode materials because C6H2Na2O6 electrode can deliver its sodium ions to a sodium‐free anode directly without any presodiation.
NGS-Based B-Cell Receptor Repertoire AnalysisRepertoire analyses in the Context of Inborn Errors of Immunity
Authors: van Schouwenburg Pauline A. , van der Burg Mirjam , IJspeert Hanna
Published: May 2022

Inborn errors of immunity (IEI) are genetic defects that can affect both the innate and the adaptive immune system. Patients with IEI usually present with recurrent infections, but many also suffer from immune dysregulation, autoimmunity, and malignancies.

Inborn errors of the immune system can cause defects in the development and selection of the B-cell receptor (BCR) repertoire. Patients with IEI can have a defect in one of the key processes of immune repertoire formation like V(D)J recombination, somatic hypermutation (SHM), class switch recombination (CSR), or (pre-)BCR signalling and proliferation. However, also other genetic defects can lead to quantitative and qualitative differences in the immune repertoire.

In this chapter, we will give an overview of protocols that can be used to study the immune repertoire in patients with IEI, provide considerations to take into account before setting up experiments, and discuss analysis of the immune repertoire data using Antigen Receptor Galaxy (ARGalaxy).
Generic Multiplex Digital PCR for Accurate Quantification of T Cells in Copy Number Stable and Unstable DNA Samples
Authors: Nell Rogier J. , Zoutman Willem H. , Versluis Mieke , van der Velden Pieter A.
Published: May 2022

An accurate T cell quantification is prognostically and therapeutically relevant in various clinical applications, including oncology care and research. In this chapter, we describe how T cell quantifications can be obtained from bulk DNA samples with a multiplex digital PCR experiment. The experimental setup includes the concurrent quantification of three different DNA targets within one reaction: a unique T cell DNA marker, a regional corrector, and a reference DNA marker. The T cell marker is biallelically absent in T cells due to VDJ rearrangements, while the reference is diploid in all cells. The so-called regional corrector allows to correct for possible copy number alterations at the T cell marker locus in cancer cells. By mathematically integrating the measurements of all three markers, T cells can be accurately quantified in both copy number stable and unstable DNA samples.
Gene Engineering T Cells with T-Cell Receptor for Adoptive Therapy
Authors: Kortleve Dian , van Brakel Mandy , Wijers Rebecca , Debets Reno , Hammerl Dora
Published: May 2022

Prior to clinical testing of adoptive T-cell therapy with T-cell receptor (TCR)-engineered T cells, TCRs need to be retrieved, annotated, gene-transferred, and extensively tested in vitro to accurately assess specificity and sensitivity of target recognition. Here, we present a fundamental series of protocols that cover critical preclinical parameters, thereby enabling the selection of candidate TCRs for clinical testing.
AIRR Community Guide to Planning and Performing AIRR-Seq Experiments
Authors: Eugster Anne , Bostick Magnolia L. , Gupta Nidhi , Mariotti-Ferrandiz Encarnita , Kraus Gloria , Meng Wenzhao , Soto Cinque , Trück Johannes , Stervbo Ulrik , Luning Prak Eline T. ,   on behalf of the AIRR Community
Published: May 2022

The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation
Authors: Babrak Lmar , Marquez Susanna , Busse Christian E. , Lees William D. , Miho Enkelejda , Ohlin Mats , Rosenfeld Aaron M. , Stervbo Ulrik , Watson Corey T. , Schramm Chaim A. ,   on behalf of the AIRR Community
Published: May 2022

High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis
Authors: Marquez Susanna , Babrak Lmar , Greiff Victor , Hoehn Kenneth B. , Lees William D. , Luning Prak Eline T. , Miho Enkelejda , Rosenfeld Aaron M. , Schramm Chaim A. , Stervbo Ulrik ,   on behalf of the AIRR Community
Published: May 2022

Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community
Authors: Rosenfeld Aaron M. , Meng Wenzhao , Horne Kalisse I. , Chen Elaine C. , Bagnara Davide , Stervbo Ulrik , Luning Prak Eline T. ,   on behalf of the AIRR Community
Published: May 2022

In this method we illustrate how to amplify, sequence, and analyze antibody/immunoglobulin (IG) heavy-chain gene rearrangements from genomic DNA that is derived from bulk populations of cells by next-generation sequencing (NGS). We focus on human source material and illustrate how bulk gDNA-based sequencing can be used to examine clonal architecture and networks in different samples that are sequenced from the same individual. Although bulk gDNA-based sequencing can be performed on both IG heavy (IGH) or kappa/lambda light (IGK/IGL) chains, we focus here on IGH gene rearrangements because IG heavy chains are more diverse, tend to harbor higher levels of somatic hypermutations (SHM), and are more reliable for clone identification and tracking. We also provide a procedure, including code, and detailed instructions for processing and annotation of the NGS data. From these data we show how to identify expanded clones, visualize the overall clonal landscape, and track clonal lineages in different samples from the same individual. This method has a broad range of applications, including the identification and monitoring of expanded clones, the analysis of blood and tissue-based clonal networks, and the study of immune responses including clonal evolution.
Next-Generation Sequencing-Based Clonality Detection of Immunoglobulin Gene Rearrangements in B-Cell Lymphoma
Authors: van Bladel Diede A. G. , van der Last-Kempkes Jessica L. M. , Scheijen Blanca , Groenen Patricia J. T. A. ,   on behalf of the EuroClonality Consortium
Published: May 2022

Immunoglobulin (IG) clonality assessment is a widely used supplementary test for the diagnosis of suspected lymphoid malignancies. The specific rearrangements of the immunoglobulin (IG) heavy and light chain genes act as a unique hallmark of a B-cell lymphoma, a feature that is used in clonality assessment. The widely used BIOMED-2/EuroClonality IG clonality assay, visualized by GeneScanning or heteroduplex analysis, has an unprecedented high detection rate because of the complementarity of this approach. However, the BIOMED-2/EuroClonality clonality assays have been developed for the assessment of specimens with optimal DNA quality. Further improvements for the assessment of samples with suboptimal DNA quality, such as from formalin-fixed paraffin-embedded (FFPE) specimens or specimens with a limited tumor burden, are required. The EuroClonality-NGS Working Group recently developed a next-generation sequencing (NGS)-based clonality assay for the detection of the IG heavy and kappa light chain rearrangements, using the same complementary approach as in the conventional assay. By employing next-generation sequencing, both the sensitivity and specificity of the clonality assay have increased, which not only is very useful for diagnostic clonality testing but also allows robust comparison of clonality patterns in a patient with multiple lymphoma’s that have suboptimal DNA quality. Here, we describe the protocols for IG-NGS clonality assessment that are compatible for Ion Torrent and Illumina sequencing platforms including pre-analytical DNA isolation, the analytical phase, and the post-analytical data analysis.
Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community
Authors: Christley Scott , Stervbo Ulrik , Cowell Lindsay G. ,   on behalf of the AIRR Community
Published: May 2022

AIRR-seq data sets are usually large and require specialized analysis methods and software tools. A typical Illumina MiSeq sequencing run generates 20–30 million 2 × 300 bp paired-end sequence reads, which roughly corresponds to 15 GB of sequence data to be processed. Other platforms like NextSeq, which is useful in projects where the full V gene is not needed, create about 400 million 2 × 150 bp paired-end reads. Because of the size of the data sets, the analysis can be computationally expensive, particularly the early analysis steps like preprocessing and gene annotation that process the majority of the sequence data. A standard desktop PC may take 3–5 days of constant processing for a single MiSeq run, so dedicated high-performance computational resources may be required.

VDJServer provides free access to high-performance computing (HPC) at the Texas Advanced Computing Center (TACC) through a graphical user interface (Christley et al. Front Immunol 9:976, 2018). VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provides access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene assignment, repertoire characterization, and repertoire comparison. Furthermore, VDJServer has parallelized execution for tools such as IgBLAST, so more compute resources are utilized as the size of the input data grows. Analysis that takes days on a desktop PC might take only a few hours on VDJServer. VDJServer is a free, publicly available, and open-source licensed resource. Here, we describe the workflow for performing immune repertoire analysis on VDJServer’s high-performance computing.
Data Sharing and Reuse: A Method by the AIRR Community
Authors: Corrie Brian D. , Christley Scott , Busse Christian E. , Cowell Lindsay G. , Neller Kira C. M. , Rubelt Florian , Schwab Nicholas ,   on behalf of the AIRR Community
Published: May 2022

High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to study the adaptive immune response via large-scale experiments. Since 2009, AIRR sequencing (AIRR-seq) has been widely applied to survey the immune state of individuals (see “The AIRR Community Guide to Repertoire Analysis” chapter for details). One of the goals of the AIRR Community is to make the resulting AIRR-seq data FAIR (Findable, Accessible, Interoperable, and Reusable) (Wilkinson et al. Sci Data 3:1–9, 2016), with a primary goal of making it easy for the research community to reuse AIRR-seq data (Breden et al. Front Immunol 8:1418, 2017; Scott and Breden. Curr Opin Syst Biol 24:71–77, 2020). The basis for this is the MiAIRR data standard (Rubelt et al. Nat Immunol 18:1274–1278, 2017). For long-term preservation, it is recommended that researchers store their sequence read data in an INSDC repository. At the same time, the AIRR Community has established the AIRR Data Commons (Christley et al. Front Big Data 3:22, 2020), a distributed set of AIRR-compliant repositories that store the critically important annotated AIRR-seq data based on the MiAIRR standard, making the data findable, interoperable, and, because the data are annotated, more valuable in its reuse. Here, we build on the other AIRR Community chapters and illustrate how these principles and standards can be incorporated into AIRR-seq data analysis workflows. We discuss the importance of careful curation of metadata to ensure reproducibility and facilitate data sharing and reuse, and we illustrate how data can be shared via the AIRR Data Commons.
IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope
Authors: Lefranc Marie-Paule , Lefranc Gérard
Published: May 2022

T-cell receptors (TR), the antigen receptors of T cells, specifically recognize peptides presented by the major histocompatibility (MH) proteins, as peptide/MH (pMH), on the cell surface. The structure characterization of the trimolecular TR/pMH complexes is crucial to the fields of immunology, vaccination, and immunotherapy. IMGT/3Dstructure-DB is the three-dimensional (3-D) structure database of IMGT®, the international ImMunoGenetics information system®. By its creation, IMGT®marks the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. The IMGT®immunoglobulin (IG) and TR gene and allele nomenclature (CLASSIFICATION axiom) and the IMGT unique numbering and IMGT/Collier-de-Perles (NUMEROTATION axiom) are the two founding breakthroughs of immunoinformatics. IMGT-ONTOLOGY concepts and IMGT Scientific chart rules generated from these axioms allowed IMGT®bridging genes, structures, and functions. IMGT/3Dstructure-DB contains 3-D structures of IG or antibodies, TR and MH proteins of the adaptive immune responses of jawed vertebrates (gnathostomata), IG or TR complexes with antigens (IG/Ag, TR/pMH), related proteins of the immune system of any species belonging to the IG and MH superfamilies, and fusion proteins for immune applications. The focus of this chapter is on the TR V domains and MH G domains and the contact analysis comparison in TR/pMH interactions. Standardized molecular characterization includes “IMGT pMH contact sites” for peptide and MH groove interactions and “IMGT paratopes and epitopes” for TR/pMH complexes. Data are available in the IMGT/3Dstructure database, at the IMGT Home pagehttp://www.imgt.org.
Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis
Authors: Galigalidou Chrysi , Zaragoza-Infante Laura , Chatzidimitriou Anastasia , Stamatopoulos Kostas , Psomopoulos Fotis , Agathangelidis Andreas
Published: May 2022

The study of antigen receptor gene repertoires using next-generation sequencing (NGS) technologies has disclosed an unprecedented depth of complexity, requiring novel computational and analytical solutions. Several bioinformatics workflows have been developed to this end, including the T-cell receptor/immunoglobulin profiler (TRIP), a web application implemented in R shiny, specifically designed for the purposes of comprehensive repertoire analysis, which is the focus of this chapter. TRIP has the potential to perform robust immunoprofiling analysis through the extraction and processing of the IMGT/HighV-Quest output, via a series of functions, ensuring the analysis of high-quality, biologically relevant data through a multilevel process of data filtering. Subsequently, it provides in-depth analysis of antigen receptor gene rearrangements, including (a) clonality assessment; (b) extraction of variable (V), diversity (D), and joining (J) gene repertoires; (c) CDR3 characterization at both the nucleotide and amino acid level; and (d) somatic hypermutation analysis, in the case of immunoglobulin gene rearrangements. Relevant to mention, TRIP enables a high level of customization through the integration of various options in key aspects of the analysis, such as clonotype definition and computation, hence allowing for flexibility without compromising on accuracy.