Top-down mass spectrometry of native proteoforms and their complexes: a community study.

The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories.

Top-down mass spectrometry of native proteoforms and their complexes: A community study.

The combination of native electrospray ionisation with top-down fragmentation in mass spectrometry allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and co-factors. While this approach is powerful, both native mass spectrometry and top-down mass spectrometry are not yet well standardised, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics (CTDP) initiated a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories.

Temperature, productivity, and habitat characteristics collectively drive lake food web structure.

While many efforts have been devoted to understand variations in food web structure among terrestrial and aquatic ecosystems, the environmental factors influencing food web structure at large spatial scales remain hardly explored. Here, we compiled biodiversity inventories to infer food web structure of 67 French lakes using an allometric niche-based model and tested how environmental variables (temperature, productivity, and habitat) influence them. By applying a multivariate analysis on 20 metrics of food web topology, we found that food web structural variations are represented by two distinct complementary and independent structural descriptors.

International Natural Procreative Technology Evaluation and Surveillance of Treatment for Subfertility (iNEST): enrollment and methods.

Study Question: What is the feasibility of a prospective protocol to follow subfertile couples being treated with natural procreative technology for up to 3 years at multiple clinical sites?

Summary Answer: Overall, clinical sites had missing data for about one-third of participants, the proportion of participants responding to follow-up questionnaires during time periods when participant compensation was available (about two-thirds) was double that of time periods when participant compensation was not available (about one-third) and follow-up information was most complete for pregnancies and births (obtained from both clinics and participants).

What Is Known Already: Several retrospective single-clinic studies from Canada, Ireland and the USA, with subfertile couples receiving restorative reproductive medicine, mostly natural procreative technology, have reported adjusted cumulative live birth rates ranging from 29% to 66%, for treatment for up to 2 years, with a mean women's age of about 35 years.

Study Design Size Duration: The international Natural Procreative Technology Evaluation and Surveillance of Treatment for Subfertility (iNEST) was designed as a multicenter, prospective cohort study, to enroll subfertile couples seeking treatment for live birth, assess baseline characteristics and follow them up for up to 3 years to report diagnoses, treatments and outcomes of pregnancy and live birth.

The Human Proteoform Project: Defining the human proteome.

Proteins are the primary effectors of function in biology, and thus, complete knowledge of their structure and properties is fundamental to deciphering function in basic and translational research. The chemical diversity of proteins is expressed in their many proteoforms, which result from combinations of genetic polymorphisms, RNA splice variants, and posttranslational modifications. This knowledge is foundational for the biological complexes and networks that control biology yet remains largely unknown.

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry.

The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications.

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.

One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass. Top-down mass spectrometry enables the analysis of intact proteins and proteoforms. Here members of the Consortium for Top-Down Proteomics provide a decision tree that guides researchers to robust protocols for mass analysis of intact proteins (antibodies, membrane proteins and others) from mixtures of varying complexity.

ProForma: A Standard Proteoform Notation.

The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, for writing the sequence of fully characterized proteoforms. ProForma provides a means to communicate any proteoform by writing the amino acid sequence using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain amino acids. The notation is unambiguous, human-readable, and can easily be parsed and written by bioinformatic tools.

Medical Students' Knowledge of Fertility Awareness-Based Methods of Family Planning.

Objective: Traditional medical school curricula have not addressed fertility awareness-based methods (FABMs) of family planning. The objective of this study was to assess (1) 3-year medical students' knowledge of FABMs of family planning, (2) their confidence in utilizing that knowledge in patient care, and (3) to implement focused education on FABMs to improve knowledge and confidence.

Methods: Third-year medical students at one institution in the United States were given a 10-question assessment at the beginning of their OB-GYN rotation.

Identification of ecological thresholds from variations in phytoplankton communities among lakes: contribution to the definition of environmental standards.

In aquatic ecosystems, the identification of ecological thresholds may be useful for managers as it can help to diagnose ecosystem health and to identify key levers to enable the success of preservation and restoration measures. A recent statistical method, gradient forest, based on random forests, was used to detect thresholds of phytoplankton community change in lakes along different environmental gradients. It performs exploratory analyses of multivariate biological and environmental data to estimate the location and importance of community thresholds along gradients.

Clinical inquiries. Menstrual disturbances in perimenopausal women: what's best?

It's best to start with nonsteroidal anti-inflammatory drugs (NSAIDs), which effectively reduce heavy menstrual bleeding. Perimenopausal women with heavy bleeding not controlled by NSAIDs, or other forms of dysfunctional uterine bleeding, can benefit from continuous, combined hormonal therapy with estrogen and progestin; hormonal therapy with estrogen and a cyclical progestin; or a cyclical progestin alone. Intrauterine devices (IUDs) containing levonorgestrel also effectively reduce bleeding and may avoid surgical intervention.

Hormone-dependent and hormone-independent control of metabolic and developmental functions of malate dehydrogenase - review.

Malate dehydrogenases (MDHs) are specific class of ubiquitous and multimeric oxidative decarboxylases with well conserved amino acid sequences in structurally important regions and with similar overall structural topology. They mostly use malate or oxaloacetate as substrates to generate pyruvate and utilize preferentially NADP or NAD as cofactor. Among species and even within an organism they differ in their subcellular localization and specificity for the cofactor.

Exploring some of the physico-chemical properties of the LAMMER protein kinase DOA of Drosophila.

Members of the highly conserved LAMMER family of protein kinases have been described in all eukaryotes. LAMMER kinases possess markedly similar peptide motifs in their kinase catalytic subdomains that are responsible for phosphotransfer and substrate interaction, suggesting that family members serve similar functions in widely diverged species. This hypothesis is supported by their phosphorylation of SR and SR-related proteins in diverged species.

What is the best way to manage GERD symptoms in the elderly?

No evidence supports one method over another in managing uncomplicated gastroesophageal reflux disease (GERD) for patients aged >65 years. For those with endoscopically documented esophagitis, proton pump inhibitors (PPIs) relieve symptoms faster than histamine H2 receptor antagonists (H2RAs) (strength of recommendation [SOR]: B, extrapolation from randomized controlled trials [RCTs]). Treating elderly patients with pantoprazole (Protonix) after resolution of acute esophagitis results in fewer relapses than with placebo (SOR: B, double-blind RCT).

A radioligand binding assay for antitubulin activity in tumor cells.

The benzamide RH-5854 is shown to be highly potent toward tumor cells and to arrest nuclear division by a highly specific covalent binding to the beta-subunit of tubulin in the colchicine binding region. Binding of 3H-RH-5854 to beta-tubulin in HCT-116 colon cancer cells is saturable and has been exploited in the development of a cell-based competitive binding assay, which allows antitubulin effects to be detected in whole cells. 3H-RH-5854 binding is strongly inhibited by preincubating the cells with compounds that bind to the colchicine site and with paclitaxel.

Regulation of cytosolic malate dehydrogenase by juvenile hormone in Drosophila melanogaster.

The Drosophila malate dehydrogenase, or malic enzyme (ME) encoded by the Men gene, is a non-mitochondrial enzyme recovered in the cytosolic fraction. By using mutation in the Men gene and deficiencies uncovering this locus, we could show that the ME activity recovered in cytosolic fractions originates exclusively from the Men gene located at map position 87D-1 on the right arm of the 3rd chromosome. We found that juvenile hormone (JH) can induce ME activity by two mechanisms.