Estimation of the membrane potential of cultured macrophages from the fast potential transient upon microelectrode entry

Analysis of membrane potential recordings upon microelectrode impalement of four types of macrophages (cell lines P388D1 and PU5-1.8, cultured mouse peritoneal macrophages, and cultured human monocytes) reveals that these cells have membrane potentials at least two times more negative than sustained potential values (E(s)) frequently reported. Upon microelectrode entry into the cell (P388D1), the recorded potential drops to a peak value (E(p)) (mean -37 mV for 50 cells, range -15 to -70 mV) within 2 ms, after which it decays to a depolarized potential (E(n)) (mean -12 mV) in about 20 ms. Thereafter, the membrane develops one or a series of slow hyperpolarizations before a final sustained membrane potential (E(s)) (mean -14 mV, range -5 to -40) is established. The mean value of the peak of the first hyperpolarization (E(h)) is -30 mV (range -10 to -55 mV). The initial fast peak transient, measured upon microelectrode entry, was first described and analyzed by Lassen et al. (Lassen, U.V., A.M. T. Nielson, L. Pape, and L. O. Simonsen, 1971, J. Membr. Biol. 6:269-288 for other change in the membrane potential from its real value before impalement to a sustained depolarized value. This was shown to be true for macrophages by two-electrode impalements of single cells. Values of E(p), E(n), E(h), E(s), and membrane resistance (R(m)) measured for the other macrophages were similar to those of P388D1. From these results we conclude that E(p) is a better estimate of the true membrane potential of macrophages than E(s), and that the slow hyperpolarizations upon impalement should be regarded as transient repolarizations back to the original membrane potentials. Thus, analysis of the initial fast impalement transient can be a valuable aid in the estimation of the membrane potential of various sorts of small isolated cells by microelectrodes.     

Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.      

Molecular evolution of a repetitive region within the per gene of Drosophila

The clock gene period (per) controls a number of biological rhythms in Drosophila. In D. melanogaster, per has a repetitive region that encodes a number of alternating threonine-glycine residues. We sequenced and compared this region from several different Drosophila species belonging to various groups within the Drosophila and Sophophora subgenera. This part of per shows a great variability in both DNA sequence and length. Furthermore, analysis of the data suggests that changes in the length of this variable region might be associated with amino acid replacements in the more conserved flanking sequences.      

Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography

Rift Valley fever virus (RVFV) is a member of the Bunyaviridae virus family (genus Phlebovirus) and is considered to be one of the most important pathogens in Africa, causing viral zoonoses in livestock and humans. Here, we report the characterization of the three-dimensional structural organization of RVFV vaccine strain MP-12 by cryoelectron tomography. Vitrified-hydrated virions were found to be spherical, with an average diameter of 100 nm. The virus glycoproteins formed cylindrical hollow spikes that clustered into distinct capsomeres. In contrast to previous assertions that RVFV is pleomorphic, the structure of RVFV MP-12 was found to be highly ordered. The three-dimensional map was resolved to a resolution of 6.1 nm, and capsomeres were observed to be arranged on the virus surface in an icosahedral lattice with clear T=12 quasisymmetry. All icosahedral symmetry axes were visible in self-rotation functions calculated using the Fourier transform of the RVFV MP-12 tomogram. To the best of our knowledge, a triangulation number of 12 had previously been reported only for Uukuniemi virus, a bunyavirus also within the Phlebovirus genus. The results presented in this study demonstrate that RVFV MP-12 possesses T=12 icosahedral symmetry and suggest that other members of the Phlebovirus genus, as well as of the Bunyaviridae family, may adopt icosahedral symmetry. Knowledge of the virus architecture may provide a structural template to develop vaccines and diagnostics, since no effective anti-RVFV treatments are available for human use.     

Viral Protein Determinants of Lassa Virus Entry and Release from Polarized Epithelial Cells

The epithelium plays a key role in the spread of Lassa virus. Transmission from rodents to humans occurs mainly via inhalation or ingestion of droplets, dust, or food contaminated with rodent urine. Here, we investigated Lassa virus infection in cultured epithelial cells and subsequent release of progeny viruses. We show that Lassa virus enters polarized Madin-Darby canine kidney (MDCK) cells mainly via the basolateral route, consistent with the basolateral localization of the cellular Lassa virus receptor α-dystroglycan. In contrast, progeny virus was efficiently released from the apical cell surface. Further, we determined the roles of the glycoprotein, matrix protein, and nucleoprotein in directed release of nascent virus. To do this, a virus-like-particle assay was developed in polarized MDCK cells based on the finding that, when expressed individually, both the glycoprotein GP and matrix protein Z form virus-like particles. We show that GP determines the apical release of Lassa virus from epithelial cells, presumably by recruiting the matrix protein Z to the site of virus assembly, which is in turn essential for nucleocapsid incorporation into virions.Lassa virus (LASV), a member of the family Arenaviridae, is a highly pathogenic agent causing hemorrhagic fever as a severe clinical manifestation. Arenaviruses are currently classified into more than 20 species, which are divided into the Old World and New World virus complexes (10). The Old World group includes the prototype lymphocytic choriomeningitis virus (LCMV) and the highly human-pathogenic viruses LASV and Lujo virus, as well as the nonpathogenic Ippy, Mobala, Mopeia, and Kodoko viruses (7, 21, 36). The New World virus complex contains among others, the hemorrhagic fever-associated Junín, Machupo, Guanarito, and Sabiá viruses and the recently discovered Chapare virus (14).With the exception of the New World virus Tacaribe virus, which was isolated from fruit bats, all arenaviruses have specific rodent species as their natural reservoirs. Rodents of the Mastomys natalensis species complex were identified as the natural host of LASV in certain countries in West Africa, including Sierra Leone, Nigeria, Guinea, and Liberia (26, 35, 49). An estimated 100,000 to 300,000 human LASV infections occur annually, of which approximately 30% result in illness, which can range from mild, flu-like symptoms to fulminant hemorrhagic fever with a mortality rate of about 16% of hospitalized cases (47, 48). Due to the severe or even fatal outcome of disease, unavailability of vaccine prophylaxis, and inadequate therapeutic treatment options, LASV is classified as a biosafety level 4 agent.The primary transmission route of LASV from its host to humans is by direct exposure to virus-containing urine, which may occur via the respiratory tract, through inhalation of infected particulates, or via ingestion of contaminated food (62). Moreover, hunting and preparation for consumption of rodents have also been identified as possible risk factors for rodent-to-human transmission of LASV (67). LASV is spread from human-to-human by contact with infectious body fluids or through nosocomial contaminations (22, 27). During the infection process, virus contacts the epithelial layers of the body and, after breaking through the epithelial tissue barrier, exploits dendritic cells for further dissemination (3, 15). It has been shown for LASV, as well as for other arenaviruses, that during the course of infection, infectious virus particles are released from epithelia into body fluids and urine (32, 45, 71).As epithelial layers play a pivotal role not only in initial virus infection but also in release of virus progeny during the early stages of infection, virus spread within the organism and virus release for further transmission, the polarity of entry and release from polarized epithelia has been studied extensively with various viruses. Virus entry in polarized cells is correlated with the apical or basolateral localization of the responsible virus receptor (24, 34, 68). Viruses that are transmitted through aerosols or surface contact with body fluids are generally thought to enter the epithelial barrier from the apical side, whereas virus infections due to injuries or transmission from animals'' bites and scratches enter epithelial cell layers from the basolateral side. Further, the spread of disease is also dependent on the directional release of the virus from epithelial cells. In general, basolateral virus budding is thought to cause systemic infections, whereas local infections are a result of viruses that are released predominantly from the apical side (69). Fitting with this model, budding of wild-type Sendai virus is restricted to the apical domain of polarized cells and causes a local respiratory infection, whereas systemic spread of a Sendai virus mutant could be attributed mainly to its bipolar virus release (66). The direction of entry and release can also be highly dependent on the type of tissue involved, as Sindbis and Semliki Forest viruses show differences in directed release in colon and thyroid gland cells (75). Similar differences in polarized virus release have also been shown for different members within a single virus family (59).In order to understand virus dissemination within the organism, it is of interest to determine on which side viruses enter and leave polarized epithelial cell layers. Here, we present data on directional LASV invasion into polarized MDCK cell culture and demonstrate a directional release of LASV from these cells. Furthermore, we have elucidated how Lassa virus proteins interact to direct budding and release of LASV progeny from epithelial cell layers.     

The genetic architecture of fitness in a seed beetle: assessing the potential for indirect genetic benefits of female choice

Background  

Quantifying the amount of standing genetic variation in fitness represents an empirical challenge. Unfortunately, the shortage of detailed studies of the genetic architecture of fitness has hampered progress in several domains of evolutionary biology. One such area is the study of sexual selection. In particular, the evolution of adaptive female choice by indirect genetic benefits relies on the presence of genetic variation for fitness. Female choice by genetic benefits fall broadly into good genes (additive) models and compatibility (non-additive) models where the strength of selection is dictated by the genetic architecture of fitness. To characterize the genetic architecture of fitness, we employed a quantitative genetic design (the diallel cross) in a population of the seed beetle Callosobruchus maculatus, which is known to exhibit post-copulatory female choice. From reciprocal crosses of inbred lines, we assayed egg production, egg-to-adult survival, and lifetime offspring production of the outbred F1 daughters (F1 productivity).     

Anatomical and chemical characteristics of the seed coat of <i>Medicago sativa</i> L. (alfalfa) cv. Baralfa 85 seeds and their association with seed dormancy

Seeds of alfalfa (Medicago sativa L.) can exhibit seedcoat imposed dormancy, which produces hard seeds within a seed lot. These seeds do not germinate because they do not imbibe water due to a barrier to water entry in the seed coat. The aim of this work was to analyze the anatomical and chemical characteristics of the testa of alfalfa seeds with respect to water permeability levels. The anatomy of seeds of the cv. Baralfa 85 was studied and structural substances, polyphenols, tannins and cutin present in the testa of seeds of different water permeability levels were determined. The anatomical characteristics of the seed coat and the proportions of components were found to determine the permeability level of the seed coat, an aspect that is associated with the physical seed dormancy level. Anatomically, increased thickness of the testa was associated with a lower permeability level. The difference may be attributed to the variation in cuticle thickness, length of macrosclereids and thickness of the cell wall, and presence and development of osteosclereids. From the physiological and chemical points of view, the mechanism of physical dormancy of the testa is explained by a greater amount of components that repel water and cement the cell wall, such as polyphenols, lignins, condensed tannins, pectic substances, and a lower proportion of cellulose and hemicellulose.     

Alternative splicing and protein function

Background  

Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data.