Analysis of ZP1 gene reveals differences in zona pellucida composition in carnivores

The zona pellucida (ZP) is an extracellular envelope that surrounds mammalian oocytes. This coat participates in the interaction between gametes, induction of the acrosome reaction, block of polyspermy and protection of the oviductal embryo. Previous studies suggested that carnivore ZP was formed by three glycoproteins (ZP2, ZP3 and ZP4), with ZP1 being a pseudogene. However, a recent study in the cat found that all four proteins were expressed. In the present study, in silico and molecular analyses were performed in several carnivores to clarify the ZP composition in this order of mammals. The in silico analysis demonstrated the presence of the ZP1 gene in five carnivores: cheetah, panda, polar bear, tiger and walrus, whereas in the Antarctic fur seal and the Weddell seal there was evidence of pseudogenisation. Molecular analysis showed the presence of four ZP transcripts in ferret ovaries (ZP1, ZP2, ZP3 and ZP4) and three in fox ovaries (ZP2, ZP3 and ZP4). Analysis of the fox ZP1 gene showed the presence of a stop codon. The results strongly suggest that all four ZP genes are expressed in most carnivores, whereas ZP1 pseudogenisation seems to have independently affected three families (Canidae, Otariidae and Phocidae) of the carnivore tree.

Effect of noise on comfort in open-plan offices: application of an assessment questionnaire

Open-plan offices account for 60% of French office workspaces. The noise levels recorded in this type of environment are much lower than those encountered in industrial workplaces. Nevertheless, surveys show that noise is considered by employees as the main source of discomfort. A first questionnaire dedicated to noise discomfort was produced in 2013 and tested on a panel made up of 217 people working in 7 French companies. Today, it also makes it possible to address the issues of fatigue related to ambient sound, but above all, the survey aims to study the differences in how ambient noise is perceived depending on the type of open-plan office. On the basis of that new version, a second survey has been conducted in 23 open-plan offices, making it possible to collect the responses from 617 employees. Most of the results of the first survey have been confirmed, with an increase in the significance of the statistical analyses. Moreover, French Standard NF S 31-199, which is currently being drafted, establishes a typology of open-plan office spaces according to the types of work done in them. Based on this typology, it appears that when dealing with the impact on noise on workers, a distinction has to be made between the types of open plan offices. Practitioner Summary: Surveys conducted in open-plan offices show that noise is considered by employees as the main source of discomfort even if the noise recorded in this type of environment is not hazardous. This work presents the result of a large survey dedicated to noise discomfort conducted in 23 open-plan offices.

Advantages of the incoherent uniform theory of diffraction for acoustic calculations in open-plan offices

Sound prediction in open-plan offices is a real challenge for room acoustics models because of the large dimensions involved and because of the complexity of the interior layout. For these reasons, the geometrical theory, based on a high frequency hypothesis, is often cited as an advantageous solution. Two types of approaches are, in general, developed under this hypothesis: the phase-included approach and the energy-based or "incoherent" approach. In this paper, comparisons are presented between calculations performed using these two approaches and measurements conducted in the laboratory where workstations were separated by low dividers and placed under ceilings that were absorbent to various extents. Particular attention was paid to processing diffraction using the uniform theory of diffraction. Narrow-band comparisons between calculations and measurements show that the phase-included model is flawed at low frequencies whenever the characteristic dimensions of the elements of the room (desk, low divider, etc.) are of the same order of magnitude as the wavelength. Conversely, the incoherent formulation, which removes the part played by the interference, gives results at least as accurate, be it in octave band or overall. Boasting very short computation times, the incoherent approach opens up interesting prospects for acoustic predictions in large open-plan offices.

Noise effect on comfort in open-space offices: development of an assessment questionnaire

It is currently accepted that noise is one of the most important annoyance factors in open-space offices. However, noise levels measured in open spaces of the tertiary sector rarely exceed 65 dB(A). It, therefore, appears necessary to develop a tool that can be used to assess the noise environment of these offices and identify the parameters to be taken into consideration when assessing the noise annoyance. This article presents a questionnaire to be filled by people working in such environment, and a case study in different open plan offices. The majority of the 237 respondents consider that the ambient noise level in their environment is high and that intelligible conversations between their colleagues represent the main source of noise annoyance. This annoyance was significantly correlated with their evaluation of sound intensity, which could not be represented by A-weighted level measurements.

A new cytotype of the African pygmy mouse Mus minutoides in Eastern Africa. Implications for the evolution of sex-autosome translocations

The African pygmy mice (genus Mus, subgenus Nannomys) are recognized for their highly conserved morphology but extensive chromosomal diversity, particularly involving sex-autosome translocations, one of the rarest chromosomal rearrangements among mammals. It has been shown that in the absence of unambiguous diagnostic morphological traits, sex-autosome translocations offer accurate taxonomic markers. For example, in Mus minutoides, irrespective of the diploid number (which ranges from 2n = 18 to 34), all specimens possess the sex-autosome translocations (X.1) and (Y.1) that are unique to this species. In this study, we describe a new cytotype that challenges this view. Males are characterized by the translocation (Y.1) only, while females carry no sex-autosome translocation, the X chromosome being acrocentric. Hence, although sex-autosome translocations (X.1) and (Y.1) are still diagnostic when one or both are present, their absence does not rule out M. minutoides. This cytotype has a large distribution, with specimens found in Tanzania and in the eastern part of South Africa. The nonpervasive distribution of Rb(X.1) provides an opportunity to investigate different evolutionary scenarios of sex-autosome translocations using a phylogenetic framework and the distribution of telomeric repeats. The results tend to support a scenario involving a reversal event, i.e., fusion then fission of Rb(X.1), and highlighted the existence of a new X1X1X2X2/X1X2Y sex chromosome system, confirming the remarkable diversity of neo-sex chromosomes and sex determination systems in the African pygmy mice.

Implementation of diffraction in a ray-tracing model for the prediction of noise in open-plan offices

Sound prediction in open-plan offices is a real challenge because of the complexity of the layout of such offices, and therefore because of the multitude of acoustic phenomena involved. One such phenomenon, of primary importance, and not the least challenging of them, is the diffraction by screens and low dividers that usually partition the workspace. This paper describes implementing the equations of the Uniform Theory of Diffraction [McNamara et al. (1990). Introduction to the Uniform Theory of Diffraction (Artech House, Boston)] in an existing ray-tracing model initially dedicated to sound prediction in industrial premises. For the purposes of validation, a series of measurements was conducted in a semi-anechoic chamber in the same manner as Wang and Bradley [(2002). Appl. Acoust. 63, 849-866] but including real desktops instead of single screens. A first phase was dedicated to controlling the quality of the installation by making comparisons with McNamara's solution for a single screen on a rigid floor. Then, the validation itself was conducted with measurements on real desktops, first without a ceiling, and then with a rigid ceiling suspended above the double desk. The results of the comparisons between calculations and measurements in this configuration have demonstrated that the model is an effective tool for predicting sound levels in an open-plan office.

Rabbit zona pellucida composition: a molecular, proteomic and phylogenetic approach

The zona pellucida (ZP) participates in sperm-egg interactions during the first steps of fertilization. Recent studies have shown that the ZP matrix of oocytes in several species is composed of four glycoproteins, designated as ZP1, ZP2, ZP3 and ZP4, rather than the three described in mouse, pig and cow. In this study, investigations were carried out to unveil a fourth glycoprotein in the rabbit (Oryctolagus cuniculus) ZP. Using total RNA isolated from rabbit ovaries, the complementary deoxyribonucleic acid (cDNA) encoding rabbit ZP1 was amplified by reverse transcribed polymerase chain reaction (RT-PCR). The ZP1 cDNA contains an open reading frame of 1825 nucleotides encoding a polypeptide of 608 amino acid residues. The deduced amino acid sequence of rabbit ZP1 showed high identity with other species: 70% identity with human and horse ZP1, and 67% identity with mouse and rat ZP1. At the proteomic level, peptides corresponding to the four proteins were detected by mass spectrometry. In addition, a molecular phylogenetic analysis of ZP1 showed that pseudogenization of this gene has occurred at least four times during the evolution of mammals. The data presented in this manuscript provide evidence, for the first time, that the rabbit ZP is composed of four glycoproteins.

Phylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species) and the two mitochondrial genes cytochrome b and 12S rRNA (17 species). The analysis of the three genes does not resolve the relationships between Mus, Apodemus, and Rattus but separates Micromys from these three genera. The analysis of the two mitochondrial regions supported an association between Apodemus and Tokudaia and indicated that these two genera are more closely related to Mus than to Rattus or Micromys. Within Apodemus, the mitochondrial data sets indicated that 8 of the 9 species analyzed can be sorted into two main groups: an Apodemus group, with A. agrarius, semotus, and peninsulae, and a Sylvaemus group, with uralensis, flavicollis, alpicola, sylvaticus, and hermonensis. The position of Apodemus mystacinus is ambiguous and might be either included in Sylvaemus or considered a distinct subgenus, Karstomys, more closely related to Sylvaemus than to Apodemus. Estimation of the divergence time for these taxa suggests a separation between 7 and 8 My ago for the three groups (mystacinus and the two subgenera Apodemus and Sylvaemus). Within each subgenus, divergence times are between 5.4 and 6 My for Apodemus and between 2.2 and 3.5 My for Sylvaemus and mystacinus.

L1 (LINE-1) retrotransposon evolution and amplification in recent human history

L1 (LINE-1) elements constitute a large family of mammalian retrotransposons that have been replicating and evolving in mammals for more than 100 Myr and now compose 20% or more of the DNA of some mammals. Here, we investigated the evolutionary dynamics of the active human Ta L1 family and found that it arose approximately 4 MYA and subsequently differentiated into two major subfamilies, Ta-0 and Ta-1, each of which contain additional subsets. Ta-1, which has not heretofore been described, is younger than Ta-0 and now accounts for at least 50% of the Ta family. Although Ta-0 contains some active elements, the Ta-1 subfamily has replaced it as the replicatively dominant subfamily in humans; 69% of the loci that contain Ta-1 inserts are polymorphic for the presence or absence of the insert in human populations, as compared with 29% of the loci that contain Ta-0 inserts. This value is 90% for loci that contain Ta-1d inserts, which are the youngest subset of Ta-1 and now account for about two thirds of the Ta-1 subfamily. The successive emergence and amplification of distinct Ta L1 subfamilies shows that L1 evolution has been as active in recent human history as it has been found to be for rodent L1 families. In addition, Ta-1 elements have been accumulating in humans at about the same rate per generation as recently evolved active rodent L1 subfamilies.

L1 (LINE-1) retrotransposable elements provide a "fossil" record of the phylogenetic history of murid rodents

The single most difficult problem in phylogenetic analysis is deciding whether a shared taxonomic character is due to common ancestry or one that appeared independently due to convergence, parallelism, or reversion to an ancestral state. Mammalian L1 retrotransposons undergo periodic amplifications in which multiple copies of the elements are interspersed in the genome. Because these elements apparently are transmitted only by inheritance and are retained in the genome, a shared L1 amplification event can only be an inherited ancestral character. We propose that L1 amplification events can be an excellent tool for analyzing mammalian evolution and demonstrate here how we addressed several refractory problems in rodent systematics using L1 DNA as a taxonomic character.

Amplification of the ancient murine Lx family of long interspersed repeated DNA occurred during the murine radiation

We identified and characterized the relics of an ancient rodent L1 family, referred to as Lx, which was extensively amplified at the time of the murine radiation about 12 million years ago, and which we showed was ancestral to the modern L1 families in rat and mouse. Here we have extended our analysis of the Lx amplification by examining more murine and nonmurine species for Lx sequences using both blot hybridization and the polymerase chain reaction for a total of 36 species. In addition we have determined the relative copy number and sequence divergence, or age, of Lx elements in representative murine genera. Our results show that while Lx sequences are confined to murine genera, the extent of the amplification was different in the different murine lineages, indicating that the amplification of Lx did not precede, but was coincident with, the murine radiation. The implications of our findings for the evolutionary dynamics of L1 families and the utility of ancestral amplification events for systematics are discussed.

Molecular evidence that the spiny mouse (Acomys) is more closely related to gerbils (Gerbillinae) than to true mice (Murinae)

Spiny mice of the genus Acomys traditionally have been classified as members of the Murinae, a subfamily of rodents that also includes rats and mice with which spiny mice share a complex set of morphological characters, including a unique molar pattern. The origin and evolution of this molar pattern, documented by many fossils from Southern Asia, support the hypothesis of the monophyly of Acomys and all other Murinae. This view has been challenged by immunological studies that have suggested that Acomys is as distantly related to mice (Mus) as are other subfamilies (e.g., hamsters: Cricetinae) of the muroid rodents. We present molecular evidence derived from DNA.DNA hybridization data that indicate that the spiny mouse Acomys and two African genera of Murinae, Uranomys and Lophuromys, constitute a monophyletic clade, a view that was recently suggested on the basis of dental characters. However, our DNA.DNA hybridization data also indicate that the spiny mice (Acomys) are more closely related to gerbils (Gerbillinae) than to the true mice and rats (Murinae) with which they have been classified. Because Acomys and the brush-furred mice Uranomys and Lophuromys share no derived morphological characters with the Gerbillinae, their murine morphology must have evolved by convergence, including the molar pattern previously considered to support the monophyly of the Murinae.