Tandem chimeric transcription as a means to increase protein diversity in the human genome

The “one-gene, one-protein” rule, coined by Beadle and Tatum, has been fundamental to molecular biology. The rule implies that the genetic complexity of an organism depends essentially on its gene number. The discovery, however, that alternative gene splicing and transcription are widespread phenomena dramatically altered our understanding of the genetic complexity of higher eukaryotic organisms; in these, a limited number of genes may potentially encode a much larger number of proteins. Here we investigate yet another phenomenon that may contribute to generate additional protein diversity. Indeed, by relying on both computational and experimental analysis, we estimate that at least 4%–5% of the tandem gene pairs in the human genome can be eventually transcribed into a single RNA sequence encoding a putative chimeric protein. While the functional significance of most of these chimeric transcripts remains to be determined, we provide strong evidence that this phenomenon does not correspond to mere technical artifacts and that it is a common mechanism with the potential of generating hundreds of additional proteins in the human genome.

Y-chromosome diversity in native mexicans reveals continental transition of genetic structure in the Americas

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.

Linguistic and maternal genetic diversity are not correlated in native mexicans

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of theAmerican continent. It has been suggested that the Mesoamerican isthmus could have played an important role in severely restricting prehistorically gene flow between North and SouthAmerica. Although the Native American component has been already described in admixedMexican populations, few studies have been carried out in native Mexican populations. In thisstudy we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to eleven different native populations from Mexico. Almost all the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1 and D1); only three of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g. extensive isolation, genetic drift and founder effects) and posterior population expansions. In agreement with this observation is the fact that Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. HaplogroupX2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure on the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.

Transmit diversity vs. spatial multiplexing in modern MIMO systems

A contemporary perspective on the tradeoff between transmit antenna diversity andspatial multiplexing is provided. It is argued that, in the context of most modern wirelesssystems and for the operating points of interest, transmission techniques that utilizeall available spatial degrees of freedom for multiplexing outperform techniques that explicitlysacrifice spatial multiplexing for diversity. In the context of such systems, therefore,there essentially is no decision to be made between transmit antenna diversity and spatialmultiplexing in MIMO communication. Reaching this conclusion, however, requires thatthe channel and some key system features be adequately modeled and that suitable performancemetrics be adopted; failure to do so may bring about starkly different conclusions. Asa specific example, this contrast is illustrated using the 3GPP Long-Term Evolution systemdesign.

On high-rate full-diversity 2x2 space-time codes with low-complexity optimum detection

The 2×2 MIMO profiles included in Mobile WiMAX specifications are Alamouti’s space-time code (STC) fortransmit diversity and spatial multiplexing (SM). The former hasfull diversity and the latter has full rate, but neither of them hasboth of these desired features. An alternative 2×2 STC, which is both full rate and full diversity, is the Golden code. It is the best known 2×2 STC, but it has a high decoding complexity. Recently, the attention was turned to the decoder complexity, this issue wasincluded in the STC design criteria, and different STCs wereproposed. In this paper, we first present a full-rate full-diversity2×2 STC design leading to substantially lower complexity ofthe optimum detector compared to the Golden code with only a slight performance loss. We provide the general optimized form of this STC and show that this scheme achieves the diversitymultiplexing frontier for square QAM signal constellations. Then, we present a variant of the proposed STC, which provides a further decrease in the detection complexity with a rate reduction of 25% and show that this provides an interesting trade-off between the Alamouti scheme and SM.

Peak and persistent excess of genetic diversity following an abrupt migration increase.

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.

Generalized low-density codes with BCH constituents for full-diversity near-outage performance

A new graph-based construction of generalized low density codes (GLD-Tanner) with binary BCH constituents is described. The proposed family of GLD codes is optimal on block erasure channels and quasi-optimal on block fading channels. Optimality is considered in the outage probability sense. Aclassical GLD code for ergodic channels (e.g., the AWGN channel,the i.i.d. Rayleigh fading channel, and the i.i.d. binary erasure channel) is built by connecting bitnodes and subcode nodes via a unique random edge permutation. In the proposed construction of full-diversity GLD codes (referred to as root GLD), bitnodes are divided into 4 classes, subcodes are divided into 2 classes, and finally both sides of the Tanner graph are linked via 4 random edge permutations. The study focuses on non-ergodic channels with two states and can be easily extended to channels with 3 states or more.

Full diversity product codes for block erasure and block fading channels

We show how to build full-diversity product codes under both iterative encoding and decoding over non-ergodic channels, in presence of block erasure and block fading. The concept of a rootcheck or a root subcode is introduced by generalizing the same principle recently invented for low-density parity-check codes. We also describe some channel related graphical properties of the new family of product codes, a familyreferred to as root product codes.

A comparison of full-rate full-diversity 2x2 space-time codes for WiMAX systems

Multiple-input multiple-output (MIMO) techniques have become an essential part of broadband wireless communications systems. For example, the recently developed IEEE 802.16e specifications for broadband wireless access include three MIMOprofiles employing 2×2 space-time codes (STCs), and two of these MIMO schemes are mandatory on the downlink of Mobile WiMAX systems. One of these has full rate, and the other has full diversity, but neither of them has both of the desired features. The third profile, namely, Matrix C, which is not mandatory, is both a full rate and a full diversity code, but it has a high decoder complexity. Recently, the attention was turned to the decodercomplexity issue and including this in the design criteria, several full-rate STCs were proposed as alternatives to Matrix C. In this paper, we review these different alternatives and compare them to Matrix C in terms of performances and the correspondingreceiver complexities.

De-hyping transmit diversity in modern MIMO cellular systems

A contemporary perspective on the tradeoff between transmit antenna diversity and spatial multi-plexing is provided. It is argued that, in the context of modern cellular systems and for the operating points of interest, transmission techniques that utilize all available spatial degrees of freedom for multiplexingoutperform techniques that explicitly sacrifice spatialmultiplexing for diversity. Reaching this conclusion, however, requires that the channel and some key system features be adequately modeled; failure to do so may bring about starkly different conclusions. As a specific example, this contrast is illustrated using the 3GPP Long-Term Evolution system design.

Phylogenetic relationships in the subfamily Psychodinae (Diptera, Psychodidae)

Thanks to recent advances in molecular systematics, our knowledge of phylogenetic relationships within the order Diptera has dramatically improved. However, relationships at lower taxonomic levels remain poorly investigated in several neglected groups, such as the highly diversified moth-fly subfamily Psychodinae (Lower Diptera), which occurs in numerous terrestrial ecosystems. In this study, we aimed to understand the phylogenetic relationships among 52 Palearctic taxa from all currently known Palearctic tribes and subtribes of this subfamily, based on mitochondrial DNA. Our results demonstrate that in light of the classical systematics of Psychodinae, none of the tribes sensu Je?ek or sensu Vaillant is monophyletic, whereas at least five of the 12 sampled genera were not monophyletic. The results presented in this study provide a valuable backbone for future work aiming at identifying morphological synapomorphies to propose a new tribal classification.

Education as a mirror of Spanish society: challenges and policies towards multiple diversity

The ways in which the dominant cultural majority frames the educationalsystem determine perceptions of its own identity and understandings ofthe ‘other.’ In this article I take a political approach, by examining themanagement of cultural diversity within Spanish education policies, treating“education as the mirror of society”. This article analyzes Spanish challengesand policies approaches towards the management of immigrationrelated diversity in education. The main finding is that there is not one approach,but several, due to both the decentralized character of the educationsystem and the multiplicity of diversity that is at stake (i.e. language,religion, culture etc.)

Dynamics of diversity within the Mossos d’Esquadra

This chapter offers a case-study of diversity and diversity policies withinthe Mossos d’Esquadra, the police force of the Catalan autonomous communityin Spain. The case is described in a comprehensive way (includingpolicies in all relevant policy areas: recruitment, retention, and promotion)and at the same time analyzed with a new analytical framework (includingthe definition of diversity, the motivation for diversity within the organisation,and the facilitation of diversity within the organisation with policies).The goal of the chapter is twofold. First, offer a deeper understanding ofthe dynamics of diversity within this police force. Second, demonstrate theacademic potential of this new analytical framework.

Strain diversity of mycobacteria isolated from pulmonary tuberculosis patients at Debre Birhan Hospital, Ethiopia.

BACKGROUND: Ethiopia ranks seventh in the list of 22 high tuberculosis (TB) burden countries, with an incidence rate of 379 cases per 100 000 population for TB all forms. However, information on the genomic diversity of Mycobacterium tuberculosis in Ethiopia is limited. OBJECTIVE: To investigate the molecular characteristics of M. tuberculosis strains implicated in pulmonary TB in the study area. METHODS AND RESULTS: A cross-sectional study was conducted using socio-demographic, clinical and culture data combined with molecular typing analysis. The proportion of TB and M. tuberculosis isolates was not associated with risk factors (P > 0.05). Of 99 sputum samples, 80.8% were culture-positive. Speciation of isolates showed that 88.8% were M. tuberculosis. Further characterisation led to the identification of 27 different spoligotype patterns of M. tuberculosis; the most dominant shared types were SIT149, SIT53 and SIT54. Of the 27 strains, three strains were new and were reported to the SITVIT database. More than two thirds of the strains belonged to the Euro-American lineage. CONCLUSION: This study shows the presence of several clusters and new strains of M. tuberculosis circulating in pulmonary TB patients in the study area, suggesting recent transmission. Nationwide studies are recommended to map the population structure of M. tuberculosis and set control measures.