MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone.

Quantitative mass spectrometry-based proteomics has become a high-throughput technology for the identification and quantification of thousands of proteins in complex biological samples. Two frequently used tools, MaxQuant and MSstats, allow for the analysis of raw data and finding proteins with differential abundance between conditions of interest. To enable accessible and reproducible quantitative proteomics analyses in a cloud environment, we have integrated MaxQuant (including TMTpro 16/18plex), Proteomics Quality Control (PTXQC), MSstats, and MSstatsTMT into the open-source Galaxy framework.

The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei.

The endoplasmic reticulum membrane complex (EMC) is a versatile complex that plays a key role in membrane protein biogenesis in the ER. Deletion of the complex has wide-ranging consequences including ER stress, disturbance in lipid transport and organelle tethering, among others. Here we report the function and organization of the evolutionarily conserved EMC (TbEMC) in the highly diverged eukaryote, Trypanosoma brucei.

Enhanced AC133-specific CAR T cell therapy induces durable remissions in mice with metastatic small cell lung cancer.

Metastatic small cell lung cancer (SCLC) is not curable. While SCLC is initially sensitive to chemotherapy, remissions are short-lived. The relapse is induced by chemotherapy-selected tumor stem cells, which express the AC133 epitope of the CD133 stem cell marker.

Retraction notice to "Enhanced AC133-specific CAR T cell therapy induces durable remissions in mice with metastatic small cell lung cancer" [Canc. Lett. 520 (2021) 385-399].

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).

patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures.

pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values.

Towards Elucidating the Rotary Mechanism of the Archaellum Machinery.

Motile archaea swim by means of a molecular machine called the archaellum. This structure consists of a filament attached to a membrane-embedded motor. The archaellum is found exclusively in members of the archaeal domain, but the core of its motor shares homology with the motor of type IV pili (T4P).

The phytochrome interacting proteins ERF55 and ERF58 repress light-induced seed germination in Arabidopsis thaliana.

Seed germination is a critical step in the life cycle of plants controlled by the phytohormones abscisic acid (ABA) and gibberellin (GA), and by phytochromes, an important class of photoreceptors in plants. Here we show that light-dependent germination is enhanced in mutants deficient in the AP2/ERF transcription factors ERF55 and ERF58. Light-activated phytochromes repress ERF55/ERF58 expression and directly bind ERF55/ERF58 to displace them from the promoter of PIF1 and SOM, genes encoding transcriptional regulators that prevent the completion of germination.

Deterministic Lateral Displacement Microfluidic Chip for Minicell Purification.

Deterministic lateral displacement (DLD) is a well-known microfluidic technique for particle separation with high potential for integration into bioreactors for therapeutic applications. Separation is based on the interaction of suspended particles in a liquid flowing through an array of microposts under low Reynolds conditions. This technique has been used previously to separate living cells of different sizes but similar shapes.

A simple pipeline for cell cycle kinetic studies in the root apical meristem.

Root system architecture ultimately depends on precise signaling between different cells and tissues in the root apical meristem (RAM) and integration with environmental cues. This study describes a simple pipeline to simultaneously determine cellular parameters, nucleus geometry, and cell cycle kinetics in the RAM. The method uses marker-free techniques for nucleus and cell boundary detection, and 5-ethynyl-2'-deoxyuridine (EdU) staining for DNA replication quantification.

Phytochrome A Mediates the Disassembly of Processing Bodies in Far-Red Light.

Phytochromes are red- and far-red light receptors that control the growth and development of plants, enabling them to respond adequately to changing light conditions. It has been shown that halted mRNAs stored in RNA granules called processing bodies are released upon light perception and contribute to the adaptation to the light environment. However, the photophysiological background of this process is largely unknown.

Spotlight on FtsZ-based cell division in Archaea.

Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota.

Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling.

Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs).

Molecular Control of Sporophyte-Gametophyte Ontogeny and Transition in Plants.

Alternation of generations between a sporophytic and gametophytic developmental stage is a feature common to all land plants. This review will discuss the evolutionary origins of these two developmental programs from unicellular eukaryotic progenitors establishing the ability to switch between haploid and diploid states. We will compare the various genetic factors that regulate this switch and highlight the mechanisms which are involved in maintaining the separation of sporophytic and gametophytic developmental programs.

Dual control of MAPK activities by AP2C1 and MKP1 MAPK phosphatases regulates defence responses in Arabidopsis.

Mitogen-activated protein kinase (MAPK) cascades transmit environmental signals and induce stress and defence responses in plants. These signalling cascades are negatively controlled by specific Ser/Thr protein phosphatases of the type 2C (PP2C) and dual-specificity phosphatase (DSP) families that inactivate stress-induced MAPKs; however, the interplay between phosphatases of these different types has remained unknown. This work reveals that different Arabidopsis MAPK phosphatases, the PP2C-type AP2C1 and the DSP-type MKP1, exhibit both specific and overlapping functions in plant stress responses.

CDC48B facilitates the intercellular trafficking of SHORT-ROOT during radial patterning in roots.

CELL DIVISION CONTROL PROTEIN48 (CDC48) is essential for membrane fusion, protein degradation, and other cellular processes. Here, we revealed the crucial role of CDC48B in regulating periclinal cell division in roots by analyzing the recessive gen1 mutant. We identified the GEN1 gene through map-based cloning and verified that GEN1 encodes CDC48B.

Natural Shifts in Endosymbionts' Occurrence and Relative Frequency in Their Ciliate Host Population.

The role of bacterial endosymbionts harbored by heterotrophic species is complex. Obligate intracellular bacteria supposedly always inflict costs as the host is the only possible provider of resources. However, several experimental studies have shown that paramecia carrying bacterial endosymbionts can benefit from their infection.

Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β.

Peroxisomes and the endoplasmic reticulum (ER) cooperate in cellular lipid metabolism. They form membrane contacts through interaction of the peroxisomal membrane protein ACBD5 (acyl-coenzyme A-binding domain protein 5) and the ER-resident protein VAPB (vesicle-associated membrane protein-associated protein B). ACBD5 binds to the major sperm protein domain of VAPB via its FFAT-like (two phenylalanines [FF] in an acidic tract) motif.

Defining the interactome of the human mitochondrial ribosome identifies SMIM4 and TMEM223 as respiratory chain assembly factors.

Human mitochondria express a genome that encodes thirteen core subunits of the oxidative phosphorylation system (OXPHOS). These proteins insert into the inner membrane co-translationally. Therefore, mitochondrial ribosomes engage with the OXA1L-insertase and membrane-associated proteins, which support membrane insertion of translation products and early assembly steps into OXPHOS complexes.

Synthetic biology landscape and community in Germany.

Despite its start in the early 2000s, synthetic biology is still overall perceived as a young discipline. In some countries, such as the US, synthetic biology is academically and industrially established, while in others, including Germany, it is still an upcoming field of research. Issues with funding schemes, commercial translation of technologies, public perception, and regulations need to be addressed to establish synthetic biology as a key discipline of the 21 century.

The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica.

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from Rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture.

Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component.

Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function.

finDr: A web server for D-peptide ligand identification.

In the rapidly expanding field of peptide therapeutics, the short half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display.