Protein fingerprinting and quantification of ß-casein variants by ultra-performance liquid chromatography-high-resolution mass spectrometry.

Infant formulations are constantly evolving as novel protein ingredients are added to make them more closely mimic the protein profile of human milk; however, precise analytical methods for characterizing and quantifying the major milk proteins in such formulations are currently lacking. This article describes an ultra-performance liquid chromatography-high-resolution mass spectrometry method for intact proteins that can efficiently detect, identify, and characterize the major milk proteins and their proteoforms (phosphorylation status, degree of glycation, genetic variants among others) in ingredients and final products, with an emphasis on detecting and quantifying specific genetic variants of ß-casein in infant formulas. Method sensitivity allows detection of ß-casein A1 in A2-based infant formulas with a limit of detection of 2% (grams of ß-casein A1 per 100 g of total ß-casein). Protein glycation affects signal intensity in a linear fashion, which permits proteins to be quantified from their mass spectrometry signals after correction according to their measured glycation index. The method was validated for the quantification of ß-casein in infant formulas. Repeatability ranged from 2 to 3% and intermediate reproducibility from 5 to 9%. Calculated ß-casein amounts ranged between 77 and 110% of the values based on formulations and published protein profiles for milk. Altogether, this method can be used for general fingerprinting as well as specific characterization and quantification of individual major milk proteins in dairy-based ingredients and products.

Plasma Heating due to Cyclic Diffusion across a Separatrix.

We observe plasma heating due to collisional diffusion across a separatrix when a magnesium ion column in a Penning-Malmberg trap is cyclically pushed back and forth across a partial trapping barrier. The barrier is an externally applied axisymmetric "squeeze" potential, which creates a velocity separatrix between trapped and passing particles. Weak ion-ion collisions then cause separatrix crossings, leading to irreversible heating. The heating rate scales as the square root of the oscillation rate times the collision frequency and thus can be dominant for low-collisionality plasmas. The particle velocity distribution function is measured with coherent laser induced fluorescence and shows passing and trapped particles having an out-of-phase response to the forced plasma oscillations.

Trapped Particle Effects in the Parametric Instability of Near-Acoustic Plasma Waves.

Quantitative experiments on the parametric decay instability of near-acoustic plasma waves provide strong evidence that trapped particles reduce the instability threshold below fluid models. At low temperatures, the broad characteristics of the parametric instability are determined by the frequency detuning of the pump and daughter wave, and the wave-wave coupling strength, surprisingly consistent with cold fluid, three-wave theories. However, at higher temperatures, trapped particle effects dominate, and the pump wave becomes unstable at half the threshold pump wave amplitude with similar exponential growth rates as for a cold plasma.

First Test of Long-Range Collisional Drag via Plasma Wave Damping.

This paper presents the first experimental confirmation of a new theory predicting enhanced drag due to long-range collisions in a magnetized plasma. The experiments measure damping of Langmuir waves in a multispecies pure ion plasma, which is dominated by interspecies collisional drag in certain regimes. The measured damping rates in these regimes exceed classical predictions of collisional drag damping by as much as an order of magnitude, but agree with the new theory.

Genetic control of branching morphogenesis during Drosophila tracheal development.

Branching morphogenesis is a widely used strategy to increase the surface area of a given organ. A number of tissues undergo branching morphogenesis during development, including the lung, kidney, vascular system and numerous glands. Until recently, very little has been known about the genetic principles underlying the branching process and about the molecules participating in organ specification and branch formation. The tracheal system of insects represents one of the best-characterised branched organs. The tracheal network provides air to most tissues and its development during embryogenesis has been studied intensively at the morphological and genetic level. More than 30 genes have been identified and ordered into sequential steps controlling branching morphogenesis. These studies have revealed a number of important principles that might be conserved in other systems.

Schnurri mediates Dpp-dependent repression of brinker transcription.

Signalling by Decapentaplegic (Dpp), a member of the TGFbeta superfamily of signalling molecules, controls many aspects of Drosophila development by activating and repressing target genes. Several essential components of the Dpp signalling pathway have been identified, including the Dpp receptors Punt and Thick veins (Tkv) as well as the cytoplasmic mediators Mad and Medea. For target genes to be activated, Dpp signalling must suppress transcription of a repressor encoded by the brinker (brk) gene. Here we show that Schnurri (Shn), a large zinc-finger protein, is essential for Dpp-mediated repression of brk transcription; in contrast, Shn is not required for target-gene activation. Thus, the Dpp signalling pathway bifurcates, downstream of the signal-mediating SMAD proteins, into a Shn-dependent pathway leading to brk repression and a Shn-independent pathway leading to gene activation. The existence of several Shn-like proteins in vertebrates and the observation that Brk functions in BMP signalling in Xenopus indicates that a similar regulatory cascade may be conserved in higher organisms.

Innate recognition of bacteria in human milk is mediated by a milk-derived highly expressed pattern recognition receptor, soluble CD14.

Little is known about innate immunity to bacteria after birth in the hitherto sterile fetal intestine. Breast-feeding has long been associated with a lower incidence of gastrointestinal infections and inflammatory and allergic diseases. We found in human breast milk a 48-kD polypeptide, which we confirmed by mass spectrometry and sequencing to be a soluble form of the bacterial pattern recognition receptor CD14 (sCD14). Milk sCD14 (m-sCD14) concentrations were up to 20-fold higher than serum sCD14 from nonpregnant, pregnant, or lactating women. In contrast, lipopolysaccharide (LPS)-binding protein was at very low levels. Mammary epithelial cells produced 48-kD sCD14. m-sCD14 mediated activation by LPS and whole bacteria of CD14 negative cells, including intestinal epithelial cells, resulting in release of innate immune response molecules. m-sCD14 was undetectable in the infant formulas and commercial (cows') milk tested, although it was present in bovine colostrum. These findings indicate a sentinel role for sCD14 in human milk during bacterial colonization of the gut, and suggest that m-sCD14 may be involved in modulating local innate and adaptive immune responses, thus controlling homeostasis in the neonatal intestine.

Phase-coherent sensing of the center-of-mass motion of trapped-ion crystals.

Trapped ions are sensitive detectors of weak forces and electric fields that excite ion motion. Here measurements of the center-of-mass motion of a trapped-ion crystal that are phase coherent with an applied weak external force are reported. These experiments are conducted far from the trap motional frequency on a two-dimensional trapped-ion crystal of approximately 100 ions, and determine the fundamental measurement imprecision of our protocol free from noise associated with the center-of-mass mode. The driven sinusoidal displacement of the crystal is detected by coupling the ion crystal motion to the internal spin degree of freedom of the ions using an oscillating spin-dependent optical dipole force. The resulting induced spin precession is proportional to the displacement amplitude of the crystal, and is measured with near-projection-noise-limited resolution. A 49 pm displacement is detected with a signal-to-noise ratio of 1 in a single experimental determination, which is an order-of-magnitude improvement over prior phase-incoherent experiments. This displacement amplitude is 40 times smaller than the zero-point fluctuations. With our repetition rate, an 8.4   pm / Hz displacement sensitivity is achieved, which implies 12   ( yN/ion ) / Hz and 77   ( µ V/m ) / Hz sensitivities to forces and electric fields, respectively. This displacement sensitivity, when applied on-resonance with the center-of-mass mode, indicates the possibility of weak force and electric field detection below 10-3 yN/ion and 1 nV/m, respectively.

A novel microtubule-binding motif identified in a high molecular weight microtubule-associated protein from Trypanosoma brucei.

The major component of the cytoskeleton of the parasitic hemoflagellate Trypanosoma brucei is a membrane skeleton which consists of a single layer of tightly spaced microtubules. This array encloses the entire cell body, and it is apposed to, and connected with, the overlying cell membrane. The microtubules of this array contain numerous microtubule-associated proteins. Prominent among those is a family of high molecular weight, repetitive proteins which consist to a large extent of tandemly arranged 38-amino acid repeat units. The binding of one of these proteins, MARP-1, to microtubules has now been characterized in vitro and in vivo. MARP-1 binds to microtubules via tubulin domains other than the COOH-termini used by microtubule-associated proteins from mammalian brain, e.g., MAP2 or Tau. In vitro binding assays using recombinant protein, as well as transfection of mammalian cell lines, have established that the repetitive 38-amino acid repeat units represent a novel microtubule-binding motif. This motif is very similar in length to those of the mammalian microtubule-associated proteins Tau, MAP2, and MAP-U, but both its sequence and charge are different. The observation that the microtubule-binding motifs both of the neural and the trypanosomal proteins are of similar length may reflect the fact that both mediate binding to the same repetitive surface, the microtubule, while their sequence and charge differences are in agreement with the observation that they interact with different domains of the tubulins.

Hox proteins meet more partners.

The Hox genes are clustered sets of homeobox-containing genes that play a central role in animal development. Recent genetic and molecular data suggest that Hox proteins interact with pre-existing homeodomain protein complexes. These complexes may help to regulate Hox activity and Hox specificity, and help cells to interpret signaling cascades during development.

Extensively hydrolysed infant formulas: Need for aligned definition of peptide size characteristics and standardisation of analytical methods.

Letter by Nutten et al. on article by Levin et al. (Levin ME, Blackhurst DM, Kirstein F, Kok D, van der Watt GF, Marais AD. Residual allergenicity of amino acid-based and extensively hydrolysed cow's milk formulas. S Afr Med J 2017;107(9):763-767. S Afr Med J 2017;107(3):258-263. https://doi.org/10.7196/SAMJ.2017.v107i9.12137); and response by Levin et al.

The structure of the homeodomain and its functional implications.

The three-dimensional structure of the homeodomain, as determined by nuclear magnetic resonance spectroscopy, reveals the presence of a helix-turn-helix motif, similar to the one found in prokaryotic gene regulatory proteins. Isolated homeodomains bind with high affinity to specific DNA sequences. Thus, the structure-function relationship is highly conserved in evolution.

Regulation of histone and beta A-globin gene expression during differentiation of chicken erythroid cells.

The expression of the genes for several histones and beta A-globin was examined in the chicken erythroid cells lineage. During the transition from CFU-(E) to the mature erythrocyte, histone H5 gradually increased fourfold in nuclei with little concomitant displacement of the H1 histones. This resulted in a 70% net increase in linker histone (H1 plus H5) content. The differential accumulation of H5 reflected (i) an increase in the transcriptional activity of the H5 gene occurring at the erythroblast stage, (ii) an apparent longer half-life of H5 mRNA, and (iii) a higher stability of the protein. Although the transcriptional activity of the histone genes (except H5) decreased with cell age, it was not tightly coupled to the S phase. On the other hand, the mRNA levels for these histones were tightly regulated during the cell cycle. Use of protein and DNA synthesis inhibitors indicated that the content of H5 mRNA was regulated at the posttranscriptional level by a control mechanism(s) differing from those for the other histones. Although the transcription rates of the H5 and beta A-globin genes were comparable, differential accumulation of beta A-globin mRNA led to a 30- to 170-fold-higher copy number of the beta A-globin mRNA as the cell matured.

Mutagenic response of Ames strains cured of their inducible Fels 1 and Fels 2 prophages.

Ames strain TA100 was cured of its Fels 1 and Fels 2 prophages to yield the corresponding nonlysogenic derivative designated TAQ100. The two monolysogenic strains corresponding to TA100 lysogenic for Fels 1 (TAQ100F1) and for Fels 2 (TAQ100F2) were also isolated. In addition, the equivalent strains lacking pKM101 and designated TAQ1535, TAQ1535F1, and TAQ1535F2 were obtained. Ames strains TA98 and TA1538 are lysogenic for Fels 2 and were observed by colony hybridization to contain cryptic Fels 1 DNA sequences. Strains corresponding to TA98 and TA1538 cured of Fels 2 were isolated and designated TAQ98F1d and TAQ1538F1d, respectively. Fels 1 grew poorly on Fels 1-cured strains, and Fels 2 grew not at all on Fels 2-cured strains. The cured strains had therefore to be identified as such by their failure to react in colony hybridization with 32P-labeled probes of Fels 1 and/or Fels 2 DNA. The specificity of the labeled probes was confirmed with the aid of the nonlysogenic Salmonella typhimurium strain Q1 and its two monolysogenic derivatives Q1 (Fels 1) and Q1 (Fels 2). The cured strains were found to respond in the same manner as did the standard Ames strains to a variety of well-known mutagens, including aflatoxin B1, 7, 12-dimethylbenz(a)anthracene, daunorubicin, 2-amino-dipyrido[1,2-a:3',2'-d]imidazole, and beta-naphthylamine. Also, mitomycin C, bleomycin, and diethylstilbestrol were nonmutagenic to TAQ100 and TAQ98F1d as they are to TA100 and TA98. Since the Fels prophages are inducible by aflatoxin B1, by daunorubicin, and by other agents, it seems that mutagenesis and Fels prophage induction occur in separate subpopulations of cells; this situation had previously been reported to occur for mutagenesis and prophage lambda induction in Escherichia coli. In any case, the Fels prophages appear to have no major influence on the mutagenic response of the Ames strains.

Development and Application of Functionalized Protein Binders in Multicellular Organisms.

Protein-protein interactions are crucial for almost all biological processes. Studying such interactions in their native environment is critical but not easy to perform. Recently developed genetically encoded protein binders were shown to function inside living cells. These molecules offer a new, direct way to assess protein function, distribution and dynamics in vivo. A widely used protein binder scaffold are the so-called nanobodies, which are derived from the variable domain of camelid heavy-chain antibodies. Another commonly used scaffold, the DARPins, is based on Ankyrin repeats. In this review, we highlight how these binders can be functionalized in order to study proteins in vivo during the development of multicellular organisms. It is to be anticipated that many more applications for such synthetic protein binders will be developed in the near future.

Homeodomain proteins in development and therapy.

Homeobox genes encode transcriptional regulators found in all organisms ranging from yeast to humans. In Drosophila, a specific class of homeobox genes, the homeotic genes, specifies the identity of certain spatial units of development. Their genomic organization, in Drosophila, as well as in vertebrates, is uniquely connected with their expression which follows a 5'-posterior-3'-anterior rule along the longitudinal body axis. The 180-bp homeobox is part of the coding sequence of these genes, and the sequence of 60 amino acids it encodes is referred to as the homeodomain. Structural analyses have shown that homeodomains consist of a helix-turn-helix motif that binds the DNA by inserting the recognition helix into the major groove of the DNA and its amino-terminal arm into the adjacent minor groove. Developmental as well as gene regulatory functions of homeobox genes are discussed, with special emphasis on one group, the Antennapedia (Antp) class homeobox genes and a representative 60-amino acid Antennapedia peptide (pAntp). In cultured neuronal cells, pAntp translocates through the membrane specifically and efficiently and accumulates in the nucleus. The internalization process is followed by a strong induction of neuronal morphological differentiation, which raises the possibility that motoneuron growth is controlled by homeodomain proteins. It has been demonstrated that chimeric peptide molecules encompassing pAntp are also captured by cultured neurons and conveyed to their nuclei. This may be of enormous interest for the internalization of drugs.

Genomic organization of the genes coding for the six main histones of the chicken: complete sequence of the H5 gene.

The organization of the genes coding for histones in the chicken has been examined, with special reference to that coding for the tissue-specific, developmentally regulated histone H5. Two recombinant phages containing sequences complementary to cloned H5 cDNA have been isolated from a genomic chicken library. The clones have been characterized by heteroduplex formation, restriction nuclease analysis, hybridization to cloned homologous histone gene probes, and DNA sequencing. Hybridization to genomic DNA has shown that there is only one copy of the H5 gene per haploid genome, whereas there are six to 11 copies of the genes for the other histones. Examination of 29 X 10(3) base-pairs of DNA sequences flanking the H5 gene has revealed the absence of any other histone genes which, although not tandemly reiterated, for the most part appear to reside in loosely organized clusters. The complete DNA sequence of the H5 gene and flanking regions, as well as the mapping of the 5'-end of its messenger RNA by primer extension with AMV reverse transcriptase, has shown that the gene has no introns and little homology to other histone genes, including those for H1.

Expression of the blistered/DSRF gene is controlled by different morphogens during Drosophila trachea and wing development.

The Drosophila serum response factor (DSRF) is expressed in the precursors of the terminal tracheal cells and in the future intervein territories of the third instar wing imaginal disc. Dissection of the DSRF regulatory region reveals that a single enhancer element, which is under the control of the fibroblast growth factor (FGF)-receptor signalling pathway, is sufficient to induce DSRF expression in the terminal tracheal cells. In contrast, two separate enhancers direct expression in distinct intervein sectors of the wing imaginal disc. One element is active in the central intervein sector and is induced by the Hedgehog signalling pathway. The other element is under the control of Decapentaplegic and is active in two separate territories, which roughly correspond to the intervein sectors flanking the central sector. Hence, each of the three characterized enhancers constitutes a molecular link between a specific territory induced by a morphogen signal and the localized expression of a gene required for the final differentiation of this territory.