Method of culturing typhoid microorganisms with automatic regulation of glucose feed]

A system of oxygen-glucose inverse relationship is not acceptable for cultivation of typhoid bacilli with a high reproductive rate and glucose utilization. The elaborated method of automatic glucose supply during typhoid bacilli cultivation permits to lead the process under the optimal conditions by pH and the residual glucose concentration.     

Flora Europaea Notulae Systematicae ad Floram Europaeam spectantes No. 20 Corrigenda et Addenda

Following the publication of the last of the series of Flora Europaea Notulae, No. 20 in the Botanical Journal of the Linnean Society , 76: 297–384 (1978), a number of additions or alterations have been drawn to our attention. These are published in continuation.     

Green fluorescent protein with tryptophan-based chromophore stable at low pH

Using directed (substitution T203Y) and subsequent random mutagenesis of the monomeric cyan fluorescent protein mTurquoise2, we obtained a protein with a tryptophan-based chromophore that fluoresces in the green region of the spectrum (excitation maximum 482 nm, emission maximum 519 nm). Fluorescence of the new protein is highly stable in a wide range of pH (pK _a 4.9), more stable than all monomeric green fluorescent proteins with a tyrosine-based chromophore.     

Spatiotemporal patterns of macrophage migration inhibitory factor (Mif) expression in the mouse placenta

Background  

Macrophage migration inhibitory factor (MIF) has special pro-inflammatory roles, affecting the functions of macrophages and lymphocytes and counter-regulating the effects of glucocorticoids on the immune response. The conspicuous expression of MIF during human implantation and early embryonic development also suggests this factor acts in reproductive functions. The overall goal of this study was to evaluate Mif expression by trophoblast and embryo placental cells during mouse pregnancy.     

Ultrastructural characteristics of the differentiation of glandular cells in the anterior pituitary gland of collared lemmings (Dicrostonyx) from the Vrangel Island

In 15.5-, 16-, 17.5-, 18.5-, 20-day-old fetuses and newborn lemmings, the ultrastructure of the anterior lobe of the hypophysis has been studied. In the parenchyma of the 15.5-day-old fetus gland, some cells containing secretory material are revealed, but they are difficult for identification, since differentiation of their organellas is not completed and polymorphism of their granules is strongly manifested. On the 17.5th day of the prenatal development TTH-, ACTH-, LH-, STH-secreting adenocytes are detected; they include secretory granules having diameters 70--100 nm, 80--150 nm, 60--140 nm and 200--400 nm, respectively. On the 18.5th day FSH-secreting cells are identified. Lactotropocytes appear on the 20th day. The anterior lobe of the hypophysis of 17.5--18.5-day-old fetuses are characterized by a high level of the secretory activity which decreases to some extent before birth. Ultrastructure of the cellular organellas in the newborn hypophysis is similar to that in a mature animal, nevertheless, the diameter of the secretory granules does not reach the size of these elements in mature individuals.     

Mycoplasma gallisepticum produces a histone-like protein that recognizes base mismatches in DNA

Mycoplasmas are the smallest known microorganisms, with drastically reduced genome sizes. One of the essential biochemical pathways lost in mycoplasmas is methylation-mediated DNA repair (MMR), which is responsible for correction of base substitutions, insertions, and deletions in both bacteria and higher organisms. We found that the histone-like protein encoded by the himA/hup_2 gene of Mycoplasma gallisepticum (mgHU) recognizes typical MMR substrates, in contrast to homologues from other species. The recognition of substitution mismatches is sequence-dependent, with affinities decreasing in the following order: CC > CT = TT > AA = AC. Insertions or deletions of one nucleotide are also specifically recognized with the following sequence-dependent preference: A = T > C. One-nucleotide lesions involving guanine are bound only weakly, and this binding is indistinguishable from binding to intact DNA. Although mgHU is dissimilar to Escherichia coli HU, expression in a slow-growing hupAB E. coli strain restores wild-type growth. The results indicate that mgHU executes all essential functions of bacterial architectural proteins. The origin and the possible role of enhanced specificity for typical MMR substrates are discussed.     

Cortical potential imaging using L-curve and GCV method to choose the regularisation parameter

Background

The electroencephalography (EEG) is an attractive and a simple technique to measure the brain activity. It is attractive due its excellent temporal resolution and simple due to its non-invasiveness and sensor design. However, the spatial resolution of EEG is reduced due to the low conducting skull. In this paper, we compute the potential distribution over the closed surface covering the brain (cortex) from the EEG scalp potential. We compare two methods – L-curve and generalised cross validation (GCV) used to obtain the regularisation parameter and also investigate the feasibility in applying such techniques to N170 component of the visually evoked potential (VEP) data.

Methods

Using the image data set of the visible human man (VHM), a finite difference method (FDM) model of the head was constructed. The EEG dataset (256-channel) used was the N170 component of the VEP. A forward transfer matrix relating the cortical potential to the scalp potential was obtained. Using Tikhonov regularisation, the potential distribution over the cortex was obtained.

Results

The cortical potential distribution for three subjects was solved using both L-curve and GCV method. A total of 18 cortical potential distributions were obtained (3 subjects with three stimuli each – fearful face, neutral face, control objects).

Conclusions

The GCV method is a more robust method compared to L-curve to find the optimal regularisation parameter. Cortical potential imaging is a reliable method to obtain the potential distribution over cortex for VEP data.

     

Computational redesign of a fluorogen activating protein with Rosetta

The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed.     

Nonglutamate pore residues in ion selection and conduction in voltage-gated Ca(2+) channels

High-affinity, intrapore binding of Ca(2+) over competing ions is the essential feature in the ion selectivity mechanism of voltage-gated Ca(2+) channels. At the same time, several million Ca(2+) ions can travel each second through the pore of a single open Ca(2+) channel. How such high Ca(2+) flux is achieved in the face of tight Ca(2+) binding is a current area of inquiry, particularly from a structural point of view. The ion selectivity locus comprises four glutamate residues within the channel's pore. These glutamates make unequal contributions to Ca(2+) binding, underscoring a role for neighboring residues in pore function. By comparing two Ca(2+) channels (the L-type alpha(1C), and the non-L-type alpha(1A)) that differ in their pore properties but only differ at a single amino acid position near the selectivity locus, we have identified the amino-terminal neighbor of the glutamate residue in motif III as a determinant of pore function. This position is more important in the function of alpha(1C) channels than in alpha(1A) channels. For a systematic series of mutations at this pore position in alpha(1C), both unitary Ba(2+) conductance and Cd(2+) block of Ba(2+) current varied with residue volume. Pore mutations designed to make alpha(1C) more like alpha(1A) and vice versa revealed that relative selectivity for Ba(2+) over K(+) depended almost solely on pore sequence and not channel type. Analysis of thermodynamic mutant cycles indicates that the motif III neighbor normally interacts in a cooperative fashion with the locus, molding the functional behavior of the pore.