Articles

A computational model of mutual antagonism in the mechano-signaling network of RhoA and nitric oxide

RhoA is a master regulator of cytoskeletal contractility, while nitric oxide (NO) is a master regulator of relaxation, e.g., vasodilation. There are multiple forms of cross-talk between the RhoA/ROCK pathway a...

Authors: Akila Surendran, C. Forbes Dewey Jr, Boon Chuan Low and Lisa Tucker-Kellogg

Intercellular transfer of mitochondrial DNA carrying metastasis-enhancing pathogenic mutations from high- to low-metastatic tumor cells and stromal cells via extracellular vesicles

Mitochondrial DNA (mtDNA) carrying certain pathogenic mutations or single nucleotide variants (SNVs) enhances the invasion and metastasis of tumor cells, and some of these mutations are homoplasmic in tumor ce...

Authors: Keizo Takenaga, Nobuko Koshikawa and Hiroki Nagase

Comparative transcriptomic analysis reveals gene regulation mediated by caspase activity in a chordate organism

Apoptosis is a caspase regulated cell death present in all metazoans defined by a conserved set of morphological features. A well-described function of apoptosis is the removal of excessive cells during develo...

Authors: Gabriel Krasovec, Anthi Karaiskou, Éric Quéinnec and Jean-Philippe Chambon

Normal seminal plasma could preserve human spermatozoa against cryopreservation damages in Oligozoospermic patients

Cryopreservation of human spermatozoa has been identified as an efficient procedure to preserve fertility in men before any cancer therapy or surgical infertility treatment. Despite the benefits of the procedu...

Authors: Fatemeh Eini, Maryam Azizi kutenaei, Maryam Hosseinzadeh Shirzeyli, Zeinolabedin Sharifian Dastjerdi, Mahmoud Omidi and Marefat Ghaffari Novin

Evaluation of selected carotenoids of Lycopersicon esculentum variants as therapeutic targets for ‘Alzheimer’s disease: an in silico approach

The seriousness and menace of the worldwide weight of ‘Alzheimer’s disease have been related to a few factors, which incorporate antioxidant system depletion, mutation of proteins, and high expression of choli...

Authors: Olalekan Olanrewaju Bakare, Adewale Oluwaseun Fadaka, Musa Oyebowale Akanbi, Kolajo Adedamola Akinyede, Ashwil Klein and Marshall Keyster

Intracellular targeting of Cisd2/Miner1 to the endoplasmic reticulum

Cisd1 and Cisd2 proteins share very similar structures with an N-terminal membrane-anchoring domain and a C-terminal cytosolic domain containing an iron-cluster binding domain and ending with a C-terminal KKxx...

Authors: Claudie Bian, Anna Marchetti, Philippe Hammel and Pierre Cosson

MDMX is essential for the regulation of p53 protein levels in the absence of a functional MDM2 C-terminal tail

MDM2 is an E3 ubiquitin ligase that is able to ubiquitinate p53, targeting it for proteasomal degradation. Its homologue MDMX does not have innate E3 activity, but is able to dimerize with MDM2. Although mouse...

Authors: Jack D. Sanford, Jing Yang, Jing Han, Laura A. Tollini, Aiwen Jin and Yanping Zhang

The 3D nuclear conformation of the major histocompatibility complex changes upon cell activation both in porcine and human macrophages

The crucial role of the major histocompatibility complex (MHC) for the immune response to infectious diseases is well-known, but no information is available on the 3D nuclear organization of this gene-dense re...

Authors: Florence Mompart, Alain Kamgoué, Yvette Lahbib-Mansais, David Robelin, Agnès Bonnet, Claire Rogel-Gaillard, Silvia Kocanova and Martine Yerle-Bouissou

Systematic identification of non-canonical transcription factor motifs

Sequence-specific transcription factors (TFs) recognize motifs of related nucleotide sequences at their DNA binding sites. Upon binding at these sites, TFs regulate critical molecular processes such as gene ex...

Authors: Luis Chumpitaz-Diaz, Md. Abul Hassan Samee and Katherine S. Pollard

An alternative D. melanogaster 7SK snRNP

The 7SK small nuclear RNA (snRNA) found in most metazoans is a key regulator of P-TEFb which in turn regulates RNA polymerase II elongation. Although its primary sequence varies in protostomes, its secondary s...

Authors: Duy Nguyen, Nicolas Buisine, Olivier Fayol, Annemieke A. Michels, Olivier Bensaude, David H. Price and Patricia Uguen

Effect of bacterial infection on sperm quality and DNA fragmentation in subfertile men with Leukocytospermia

Although bacterial infections have been recognized as a possible cause of male infertility, the effect of bacterial infections on sperm quality and sperm DNA fragmentation remains controversial. The current st...

Authors: Fatemeh Eini, Maryam Azizi Kutenaei, Fayegheh Zareei, Zeinolabedin Sharifian Dastjerdi, Maryam Hosseinzadeh Shirzeyli and Ensieh Salehi

SH3BGRL3 binds to myosin 1c in a calcium dependent manner and modulates migration in the MDA-MB-231 cell line

The human SH3 domain Binding Glutamic acid Rich Like 3 (SH3BGRL3) gene is highly conserved in phylogeny and widely expressed in human tissues. However, its function is largely undetermined. The protein was found ...

Authors: Filippo Di Pisa, Elisa Pesenti, Maria Bono, Andrea N. Mazzarello, Cinzia Bernardi, Michael P. Lisanti, Giovanni Renzone, Andrea Scaloni, Ermanno Ciccone, Franco Fais, Silvia Bruno, Paolo Scartezzini and Fabio Ghiotto

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity

In retinal degenerative disease, progressive and debilitating conditions result in deterioration of retinal cells and visual loss. In human, retina lacks the inherent capacity for regeneration. Therefore, rege...

Authors: Atefeh Atefi, Pendar Shojaei Kojouri, Fereshteh Karamali, Shiva Irani and Mohammad Hossein Nasr-Esfahani

Cell-in-cell phenomenon: leukocyte engulfment by non-tumorigenic cells and cancer cell lines

Research on cell-in-cell (CIC) phenomena, including entosis, emperipolesis and cannibalism, and their biological implications has increased in recent years. Homotypic and heterotypic engulfment of various targ...

Authors: Mareike F. Bauer, Michael Hader, Markus Hecht, Maike Büttner-Herold, Rainer Fietkau and Luitpold V. R. Distel

Disruption of Drosophila larval muscle structure and function by UNC45 knockdown

Proper muscle function is heavily dependent on highly ordered protein complexes. UNC45 is a USC (named since this region is shared by three proteins UNC45/CRO1/She4P) chaperone that is necessary for myosin inc...

Authors: Abiramy Karunendiran, Christine T. Nguyen, Virginijus Barzda and Bryan A. Stewart

Chick fetal organ spheroids as a model to study development and disease

Organ culture models have been used over the past few decades to study development and disease. The in vitro three-dimensional (3D) culture system of organoids is well known, however, these 3D systems are both...

Authors: Soran Dakhel, Wayne I. L. Davies, Justin V. Joseph, Tushar Tomar, Silvia Remeseiro and Lena Gunhaga

Effects of temperature on proliferation of myoblasts from donor piglets with different thermoregulatory maturities

Climate change and the associated risk for the occurrence of extreme temperature events or permanent changes in ambient temperature are important in the husbandry of farm animals. The aim of our study was to i...

Authors: Katharina Metzger, Dirk Dannenberger, Armin Tuchscherer, Siriluck Ponsuksili and Claudia Kalbe

Complex II subunit SDHD is critical for cell growth and metabolism, which can be partially restored with a synthetic ubiquinone analog

Succinate dehydrogenase (Complex II) plays a dual role in respiration by catalyzing the oxidation of succinate to fumarate in the mitochondrial Krebs cycle and transferring electrons from succinate to ubiquino...

Authors: Aloka B. Bandara, Joshua C. Drake and David A. Brown

Genotype-determined EGFR-RTK heterodimerization and its effects on drug resistance in lung Cancer treatment revealed by molecular dynamics simulations

Epidermal growth factor receptor (EGFR) and its signaling pathways play a vital role in pathogenesis of lung cancer. By disturbing EGFR signaling, mutations of EGFR may lead to progression of cancer or the eme...

Authors: Mengxu Zhu, Debby D. Wang and Hong Yan

Effect of Voacamine upon inhibition of hypoxia induced fatty acid synthesis in a rat model of methyln-nitrosourea induced mammary gland carcinoma

In the present study, fatty acid synthesis is targeted to combat mammary gland carcinoma by activating prolyl hydroxylase-2 with Voacamine alone and in combination with Tamoxifen. It was hypothesized that the ...

Authors: Lakhveer Singh, Manjari Singh, Shubham Rastogi, Anurag Choudhary, Dinesh Kumar, Ritu Raj, Mohd Nazam Ansari, Abdulaziz S. Saeedan and Gaurav Kaithwas

Methodology for comprehensive cell-level analysis of wound healing experiments using deep learning in MATLAB

Endothelial healing after deployment of cardiovascular devices is particularly important in the context of clinical outcome. It is therefore of great interest to develop tools for a precise prediction of endot...

Authors: Jan Oldenburg, Lisa Maletzki, Anne Strohbach, Paul Bellé, Stefan Siewert, Raila Busch, Stephan B. Felix, Klaus-Peter Schmitz and Michael Stiehm

Retraction Note: Evaluation of PAX8 expression promotes the proliferation of stomach Cancer cells

Authors: Liang-Yu Bie, Ning Li, Wen-Ying Deng, Xiao-Yu Lu, Ping Guo and Su-Xia Luo

sFLT01 modulates invasion and metastasis in prostate cancer DU145 cells by inhibition of VEGF/GRP78/MMP2&9 axis

About 90% of cancer-related deaths are due to metastasis of cancer cells, and angiogenesis is a critical step in this process. sFLT01 is a novel fusion protein and a dual-targeting agent that neutralizes both ...

Authors: Sepideh Taghizadeh, Zahra-Soheila Soheili, Mehdi Sadeghi, Shahram Samiei, Ehsan Ranaei Pirmardan, Ali Kashanian, Fahimeh Zakeri, Hamid Latifi-Navid and Hoda Shams Najafabadi

Impact of uORFs in mediating regulation of translation in stress conditions

A large fraction of genes contains upstream ORFs (uORFs) in the 5′ untranslated region (5’UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing prematur...

Authors: Simone G. Moro, Cedric Hermans, Jorge Ruiz-Orera and M. Mar Albà

Novel leukocyte-depleted platelet-rich plasma-based skin equivalent as an in vitro model of chronic wounds: a preliminary study

Chronic leg ulcerations are associated with Haemoglobin disorders, Type2 Diabetes Mellitus, and long-term venous insufficiency, where poor perfusion and altered metabolism develop into a chronic inflammation t...

Authors: Elisa Seria, George Galea, Joseph Borg, Kevin Schembri, Gabriella Grech, Sarah Samut Tagliaferro and Alexander Felice

Assessing nucleic acid binding activity of four dinoflagellate cold shock domain proteins from Symbiodinium kawagutii and Lingulodinium polyedra

Dinoflagellates have a generally large number of genes but only a small percentage of these are annotated as transcription factors. Cold shock domain (CSD) containing proteins (CSPs) account for roughly 60% of...

Authors: Bahareh Zaheri and David Morse

The Glypican proteoglycans show intrinsic interactions with Wnt-3a in human prostate cancer cells that are not always associated with cascade activation

Prostate cancer occurs through multiple steps until advanced metastasis. Signaling pathways studies can result in the identification of targets to interrupt cancer progression. Glypicans are cell surface prote...

Authors: Gabrielle Ferrante Alves de Moraes, Eduardo Listik, Giselle Zenker Justo, Carolina Meloni Vicente and Leny Toma

SEM and TEM for identification of capsular fibrosis and cellular behavior around breast implants – a descriptive analysis

Capsular fibrosis (CF) is the most common long-term complication in implant-based breast augmentation. It is well accepted that the foreign body response (FBR) instigates the development of fibrotic disease. O...

Authors: Britta Kuehlmann, Isabel Zucal, Clark Andrew Bonham, Lydia-Marie Joubert and Lukas Prantl

Uncarboxylated osteocalcin alleviates the inhibitory effect of high glucose on osteogenic differentiation of mouse bone marrow–derived mesenchymal stem cells by regulating TP63

Progressive population aging has contributed to the increased global prevalence of diabetes and osteoporosis. Inhibition of osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) by hyperglyc...

Authors: Fangzi Gong, Le Gao, Luyao Ma, Guangxin Li and Jianhong Yang

Online biophysical predictions for SARS-CoV-2 proteins

The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural bi...

Authors: Luciano Kagami, Joel Roca-Martínez, Jose Gavaldá-García, Pathmanaban Ramasamy, K. Anton Feenstra and Wim F. Vranken

Association of Sonic Hedgehog with the extracellular matrix requires its zinc-coordination center

Sonic Hedgehog (Shh) has a catalytic cleft characteristic for zinc metallopeptidases and has significant sequence similarities with some bacterial peptidoglycan metallopeptidases defining a subgroup within the...

Authors: Carina Jägers and Henk Roelink

Cyr61 promotes Schwann cell proliferation and migration via αvβ3 integrin

Schwann cells (SCs) play a crucial role in the repair of peripheral nerves. This is due to their ability to proliferate, migrate, and provide trophic support to axon regrowth. During peripheral nerve injury, S...

Authors: Zhenghui Cheng, Yawen Zhang, Yinchao Tian, Yuhan Chen, Fei Ding, Han Wu, Yuhua Ji and Mi Shen

A cell-based ribozyme reporter system employing a chromosomally-integrated 5′ exonuclease gene

Bioinformatic genome surveys indicate that self-cleaving ribonucleic acids (ribozymes) appear to be widespread among all domains of life, although the functions of only a small number have been validated by bi...

Authors: Aiyada Aroonsri, Jindaporn Kongsee, Jeremy David Gunawan, Daniel Abidin Aubry and Philip James Shaw

Responsiveness of human bronchial fibroblasts and epithelial cells from asthmatic and non-asthmatic donors to the transforming growth factor-β₁ in epithelial-mesenchymal trophic unit model

The asthma-related airway wall remodeling is associated i.a. with a damage of bronchial epithelium and subepithelial fibrosis. Functional interactions between human bronchial epithelial cells and human bronchi...

Authors: Milena Paw, Dawid Wnuk, Bogdan Jakieła, Grażyna Bochenek, Krzysztof Sładek, Zbigniew Madeja and Marta Michalik

Intracellular pH regulation: characterization and functional investigation of H⁺ transporters in Stylophora pistillata

Reef-building corals regularly experience changes in intra- and extracellular H⁺ concentrations ([H⁺]) due to physiological and environmental processes. Stringent control of [H⁺] is required to maintain the homeo...

Authors: Laura Capasso, Philippe Ganot, Víctor Planas-Bielsa, Sylvie Tambutté and Didier Zoccola

SPRD: a surface plasmon resonance database of common factors for better experimental planning

Surface plasmon resonance is a label-free biophysical technique that is widely used in investigating biomolecular interactions, including protein-protein, protein-DNA, and protein-small molecule binding. Surfa...

Authors: Purushottam B. Tiwari, Camelia Bencheqroun, Mario Lemus, Taryn Shaw, Marilyn Kouassi-Brou, Adil Alaoui and Aykut Üren

STAU2 protein level is controlled by caspases and the CHK1 pathway and regulates cell cycle progression in the non-transformed hTERT-RPE1 cells

Staufen2 (STAU2) is an RNA binding protein involved in the posttranscriptional regulation of gene expression. In neurons, STAU2 is required to maintain the balance between differentiation and proliferation of ...

Authors: Lionel Condé, Yulemi Gonzalez Quesada, Florence Bonnet-Magnaval, Rémy Beaujois and Luc DesGroseillers

Fetal sex modulates placental microRNA expression, potential microRNA-mRNA interactions, and levels of amino acid transporter expression and substrates: INFAT study subpopulation analysis of n-3 LCPUFA intervention during pregnancy and associations with offspring body composition

Previously, we revealed sexually dimorphic mRNA expression and responsiveness to maternal dietary supplementation with n-3 long-chain polyunsaturated fatty acids (LCPUFA) in placentas from a defined INFAT stud...

Authors: Eva-Maria Sedlmeier, Dorothy M. Meyer, Lynne Stecher, Manuela Sailer, Hannelore Daniel, Hans Hauner and Bernhard L. Bader

Correction to: Avian eggshell biomineralization: an update on its structure, mineralogy and protein tool kit

An amendment to this paper has been published and can be accessed via the original article.

Authors: J. Gautron, L. Stapane, N. Le Roy, Y. Nys, A. B. Rodriguez-Navarro and M. T. Hincke

Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation

Human induced pluripotent stem cells (iPSC) have opened new avenues for regenerative medicine. Consequently, iPSC-derived motor neurons have emerged as potentially viable therapies for spinal cord injuries and...

Authors: Emilia Solomon, Katie Davis-Anderson, Blake Hovde, Sofiya Micheva-Viteva, Jennifer Foster Harris, Scott Twary and Rashi Iyer

Isolation, culture, and characterization of chicken intestinal epithelial cells

Enterocytes exert an absorptive and protective function in the intestine, and they encounter many different challenging factors such as feed, bacteria, and parasites. An intestinal epithelial in vitro model ca...

Authors: Federico Ghiselli, Barbara Rossi, Martina Felici, Maria Parigi, Giovanni Tosi, Laura Fiorentini, Paola Massi, Andrea Piva and Ester Grilli

Avian eggshell biomineralization: an update on its structure, mineralogy and protein tool kit

The avian eggshell is a natural protective envelope that relies on the phenomenon of biomineralization for its formation. The shell is made of calcium carbonate in the form of calcite, which contains hundreds ...

Authors: J. Gautron, L. Stapane, N. Le Roy, Y. Nys, A. B. Rodriguez-Navarro and M. T. Hincke

Increased expression of MUSASHI1 in epithelial breast cancer cells is due to down regulation of miR-125b

Musashi1 (MSI1) is an oncogenic protein with a crucial role in the proliferation and characteristics of the epithelial cells in breast cancer. The change in expression of MSI1 has a role in solid tumor progressio...

Authors: Mahboobeh Forouzanfar, Liana Lachinani, Kianoush Dormiani, Mohammad Hossein Nasr-Esfahani and Kamran Ghaedi

Identification and characterization of the LRR repeats in plant LRR-RLKs

Leucine-rich-repeat receptor-like kinases (LRR-RLKs) play central roles in sensing various signals to regulate plant development and environmental responses. The extracellular domains (ECDs) of plant LRR-RLKs ...

Authors: Tianshu Chen

The negative charge of the 343 site is essential for maintaining physiological functions of CXCR4

Warts, hypogammaglobulinemia, recurrent bacterial infections and myelokathexis (WHIM) syndrome is a primary immunodeficiency disease (PID) usually caused by autosomal dominant mutations in the chemokine receptor

Authors: Liqing Wang, Qiuhong Xiong, Ping Li, Guangxin Chen, Nayab Tariq and Changxin Wu

Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

One striking feature of the large KRAB domain-containing zinc finger protein (KZFP) family is its rapid evolution, leading to hundreds of member genes with various origination time in a certain mammalian genom...

Authors: Pan Shen, Aishi Xu, Yushan Hou, Huqiang Wang, Chao Gao, Fuchu He and Dong Yang

circRNA_0005529 facilitates growth and metastasis of gastric cancer via regulating miR-527/Sp1 axis

Circular RNAs (circRNAs) are endogenous non-coding RNAs, which are associated with various biological processes, including microRNA (miRNA) interaction, protein binding and regulatory splicing. circRNA_0005529...

Authors: Xing Zhang, Hongwei Yang, Yingdong Jia, Zhengwen Xu, Liuping Zhang, Meng Sun and Jing Fu

NanoSIMS observations of mouse retinal cells reveal strict metabolic controls on nitrogen turnover

Most of the cells of the mammalian retina are terminally differentiated, and do not regenerate once fully developed. This implies that these cells have strict controls over their metabolic processes, including...

Authors: Elisa A. Bonnin, Eugenio F. Fornasiero, Felix Lange, Christoph W. Turck and Silvio O. Rizzoli

New genotypes of Helicobacter Pylori VacA d-region identified from global strains

Pathogenesis of Helicobacter Pylori (HP) vacuolating toxin A (vacA) depends on polymorphic diversity within the signal (s), middle (m), intermediate (i), deletion (d) and c-regions. These regions show distinct al...

Authors: Djaleel Muhammad Soyfoo, Yussriya Hanaa Doomah, Dong Xu, Chao Zhang, Huai-Ming Sang, Yan-Yan Liu, Guo-Xin Zhang, Jian-Xia Jiang and Shun-Fu Xu

Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization

Human ether-à-go-go-related gene potassium channel 1 (hERG) is a voltage-gated potassium channel, the voltage-sensing domain (VSD) of which is targeted by a gating-modifier toxin, APETx1. APETx1 is a 42-residue p...

Authors: Kazuki Matsumura, Takushi Shimomura, Yoshihiro Kubo, Takayuki Oka, Naohiro Kobayashi, Shunsuke Imai, Naomi Yanase, Madoka Akimoto, Masahiro Fukuda, Mariko Yokogawa, Kazuyoshi Ikeda, Jun-ichi Kurita, Yoshifumi Nishimura, Ichio Shimada and Masanori Osawa