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La conservación enfocada en especies endémicas es prioritaria dada su alta vulnerabilidad. Para lograrla resulta imprescindible conocer la historia natural de las especies. El Gorrión Serrano (Xenospiza baileyi), catalogado en peligro de extinción, es una de las aves endémicas más vulnerables de México (valor de vulnerabilidad máximo = 20). Su estudio ha sido intermitente y la información asociada a su historia natural se encuentra dispersa, no publicada o es de difícil acceso. En este trabajo se sistematizó, examinó y actualizó el conocimiento relacionado con la historia natural de X. baileyi. Se compilaron estudios sobre esta especie para identificar vacíos en torno a su investigación. Se lograron integrar aspectos de la historia natural de X. baileyi relacionados con su taxonomía, descripción, distribución, hábitat, demografía, dispersión, territorialidad, alimentación, interacciones ecológicas, perchas, vocalizaciones, ciclo reproductivo, cortejo, nido, huevos, pollos y amenazas. Además, se incluyó información nueva resultante de actividades de monitoreo comunitario sobre esta especie, lo cual permitió denotar la importancia de la inclusión comunitaria para el manejo y conservación de la especie y su hábitat. Esta información resulta fundamental para optimizar su estudio y orientar las acciones urgentes en torno a su conservación.

The Sierra Madre Sparrow (Xenospiza baileyi) is an endangered species microendemic to subalpine grasslands of central and northwestern Mexico. Given that land use change is highly dynamic in central Mexico, there is a need for a continuous monitoring of the distribution and conservation status of the species across the region. We here update the distribution of the Sierra Madre Sparrow by surveying the historical sites where the species is known to occur, verifying records from a citizen science database, and identifying potential habitat in the region to find new localities for the species. We also highlight main local threats and discuss potential conservation activities for the sites where we recorded the species. We found that all historical sites are still inhabited by the species and we identified new localities for the Sierra Madre Sparrow. Each locality presents particular threats for the conservation of the species. Common threats to all sites include agriculture and land owners' unawareness about the presence of the species. Particular attention should be focused on providing management guidelines for agricultural practices in the area. Special efforts must be directed to engaging communities into conserving and monitoring subalpine grasslands. Much work should be done to define and apply conservation strategies in cooperation with local governments, institutions, and communities. The identification of new localities for the species reveals the need to expand research beyond traditional study and bird-watching sites.

The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent-offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use.

We have entered the era of individual genomic sequencing, and can already see exponential progress in the field. It is of utmost importance to exclude false-positive variants from reported datasets. However, because of the nature of the used algorithms, this task has not been optimized to the required level of precision. This study presents a unique strategy for identifying SNPs, called COIN-VGH, that largely minimizes the presence of false-positives in the generated data. The algorithm was developed using the X-chromosome–specific regions from the previously sequenced genomes of Craig Venter and James Watson. The algorithm is based on the concept that a nucleotide can be individualized if it is analyzed in the context of its surrounding genomic sequence. COIN-VGH consists of defining the most comprehensive set of nucleotide strings of a defined length that map with 100% identity to a unique position within the human reference genome (HRG). Such set is used to retrieve sequence reads from a query genome (QG), allowing the production of a genomic landscape that represents a draft HRG-guided assembly of the QG. This landscape is analyzed for specific signatures that indicate the presence of SNPs. The fidelity of the variation signature was assessed using simulation experiments by virtually altering the HRG at defined positions. Finally, the signature regions identified in the HRG and in the QG reads are aligned and the precise nature and position of the corresponding SNPs are detected. The advantages of COIN-VGH over previous algorithms are discussed.

Several lines of evidence suggest that reiterated sequences in the human genome are targets for nonallelic homologous recombination (NAHR), which facilitates genomic rearrangements. We have used a PCR-based approach to identify breakpoint regions of rearranged structures in the human genome. In particular, we have identified intrachromosomal identical repeats that are located in reverse orientation, which may lead to chromosomal inversions. A bioinformatic workflow pathway to select appropriate regions for analysis was developed. Three such regions overlapping with known human genes, located on chromosomes 3, 15, and 19, were analyzed. The relative proportion of wild-type to rearranged structures was determined in DNA samples from blood obtained from different, unrelated individuals. The results obtained indicate that recurrent genomic rearrangements occur at relatively high frequency in somatic cells. Interestingly, the rearrangements studied were significantly more abundant in adults than in newborn individuals, suggesting that such DNA rearrangements might start to appear during embryogenesis or fetal life and continue to accumulate after birth. The relevance of our results in regard to human genomic variation is discussed.

The comparative analysis of genomic characteristics and single-nucleotide polymorphism patterns from large fragments borne on different replicons of Sinorhizobium spp. genomes clearly demonstrate that DNA recombination among closely related bacteria is a major event in the diversification of this genome, especially in pSymA, resulting in mosaic structure.

Background Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB) of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs). By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation.

Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification.

To confirm the immunogenicity and tolerance of the inactivated, fractionated, and purified influenza vaccine, in a Mexican adult population aged 55 and older, medically served at a Petróleos Mexicanos Hospital (Pemex, Mexican Oil Company).The study was conducted between November and December, 2000, among ninety adult subjects aged 55 years and older who were seen at the Hospital Central Sur Pemex. The primary endpoints regarding immunogenicity were the percentage of individuals with protective antibodies targeting hemagglutinins higher than or equal to 1:40, and the percentage of subjects who seroconverted as measured by a four-fold increase in protective antibody production. Secondary endpoints included the frequency of local and systemic reactions to the vaccine. An additional criterion that was evaluated included antigen-antibody affinity assays to measure the polyclonal antibody response to the vaccine and the specific generation of high-affinity antibodies to viral proteins, before and after vaccination.The antibody protection rate was 95.6% against the HINI strain, 98.9% against the H3N2 strain, and a 100% against the B/Yamanashi strain. Seroconversion to the HINI strain was elicited in 74.4% of subjects, to the H3N2 strain in 88.9%, and to the B/Yamanashi strain in 82.2%. Eighteen (20%) subjects developed local reactions; 17 (18.8%) developed a systemic reaction post vaccination at day 5 and nine subjects (10%) at day 28. Local reactions consisted of pain in 10 (11.1%) subjects, redness in 8 (8.8%), and induration in 6 (6.6%). General malaise, headache, and fever were identified in 10, 8.8, and 0% of subjects, respectively, at day 5, and in 4.4, 6.6, and 0%, respectively, at day 28.Influenza vaccine was highly immunogenic in a healthy Mexican adult population aged 55 years and older. The generation of high-affinity antibodies to the virus after vaccination was also demonstrated. Local and systemic adverse reactions to the vaccine identified in our study were similar to those in previous reports. The results of this study can be extrapolated to other health institutions serving this adult population to increase influenza vaccine coverage rates.

Pneumonia is the principal cause of morbidity and mortality in PEMEX medical services. Vaccination against influenza is 72% effective in preventing hospitalizations and 87% effective in preventing deaths related to this virus, and vaccination against pneumococcus is 60% effective in preventing invasive diseases by this microorganism. ACIP recommends use of both vaccines simultaneously in adults over 65 years of age.To describe the frequency, duration and severity of local and systemic reactions related to the simultaneous administration of vaccines against influenza and pneumococcus in adults over 55 years of age, and compare with reactions related to influenza vaccine.Two hundred-thirty two adults over 55 years of age were randomly assigned to two groups, group A (114 subjects) received influenza vaccine, group B (118 subjects) received influenza and pneumococcus vaccines simultaneously.Comparing the number of subjects with local reactions on the right arm between groups A and B (17 subjects vs. 27 subjects), differences were not statistically significative (p = 0.121). Systemic reactions were not statistically significative either (p = 0.126) when results were compared between both groups (30 from group A vs. 42 for group B).Simultaneous administration of influenza and pneumococcus vaccines has proven to be safety. In the absence of contraindications, there is no reason for not offering both vaccines in the same medical visit.