ENSO effects on the relationship between aerosols and evapotranspiration in the south of the Amazon biome.

The effects of the El Nino-Southern Oscillation (ENSO) events have local, regional, and global consequences for water regimes, causing floods or extreme drought events. Tropical forests are strongly affected by ENSO, and in the case of the Amazon, its territorial extension allows for a wide variation of these effects. The prolongation of drought events in the Amazon basin contributes to an increase in gas and aerosol particle emissions mainly caused by biomass burning, which in turn alter radiative fluxes and evapotranspiration rates, cyclically interfering with the hydrological regime. The ENSO effects on the interactions between aerosol particles and evapotranspiration is a critical aspect to be systematically investigated. Therefore, this study aimed to evaluate the ENSO effect on a site located on the southern portion of the Amazonian region. In addition to quantifying and testing possible differences between aerosols and evapotranspiration under different ENSO classes (El Niño, La Niña and Neutrality), this study also evaluated possible variations in evapotranspiration as a function of the aerosol load. A highly significant difference was found for air temperature, relative humidity and aerosol load between the El Niño and La Niña classes. For evapotranspiration, significant differences were found for the El Niño and La Niña classes and for El Niño and Neutrality classes. Under the Neutrality class, the aerosol load correlated significantly with evapotranspiration, explaining 20% of the phenomenon. Under the El Niño and La Niña classes, no significant linear correlation was found between aerosol load and evapotranspiration. However, the results showed that for the total data set, there is a positive and significant correlation between aerosol and evapotranspiration. It increases with a quadratic fit, i.e., the aerosol favors evapotranspiration rates up to a certain concentration threshold. The results obtained in this study can help to understand the effects of ENSO events on atmospheric conditions in the southern Amazon basin, in addition to elucidating the role of aerosols in feedback to the water cycle in the region.

Perfect Match Genomic Landscape strategy: Refinement and customization of reference genomes.

When addressing a genomic question, having a reliable and adequate reference genome is of utmost importance. This drives the necessity to refine and customize reference genomes (RGs). Our laboratory has recently developed a strategy, the Perfect Match Genomic Landscape (PMGL), to detect variation between genomes [K. Palacios-Flores et al.Genetics 208, 1631-1641 (2018)]. The PMGL is precise and sensitive and, in contrast to most currently used algorithms, is nonstatistical in nature. Here we demonstrate the power of PMGL to refine and customize RGs. As a proof-of-concept, we refined different versions of the Saccharomyces cerevisiae RG. We applied the automatic PMGL pipeline to refine the genomes of microorganisms belonging to the three domains of life: the archaea Methanococcus maripaludis and Pyrococcus furiosus; the bacteria Escherichia coli, Staphylococcus aureus, and Bacillus subtilis; and the eukarya Schizosaccharomyces pombe, Aspergillus oryzae, and several strains of Saccharomyces paradoxus. We analyzed the reference genome of the virus SARS-CoV-2 and previously published viral genomes from patients' samples with COVID-19. We performed a mutation-accumulation experiment in E. coli and show that the PMGL strategy can detect specific mutations generated at any desired step of the whole procedure. We propose that PMGL can be used as a final step for the refinement and customization of any haploid genome, independently of the strategies and algorithms used in its assembly.

Prediction and identification of recurrent genomic rearrangements that generate chimeric chromosomes in Saccharomyces cerevisiae.

Genomes are dynamic structures. Different mechanisms participate in the generation of genomic rearrangements. One of them is nonallelic homologous recombination (NAHR). This rearrangement is generated by recombination between pairs of repeated sequences with high identity. We analyzed rearrangements mediated by repeated sequences located in different chromosomes. Such rearrangements generate chimeric chromosomes. Potential rearrangements were predicted by localizing interchromosomal identical repeated sequences along the nuclear genome of the Saccharomyces cerevisiae S288C strain. Rearrangements were identified by a PCR-based experimental strategy. PCR primers are located in the unique regions bordering each repeated region of interest. When the PCR is performed using forward primers from one chromosome and reverse primers from another chromosome, the break point of the chimeric chromosome structure is revealed. In all cases analyzed, the corresponding chimeric structures were found. Furthermore, the nucleotide sequence of chimeric structures was obtained, and the origin of the unique regions bordering the repeated sequence was located in the expected chromosomes, using the perfect-match genomic landscape strategy (PMGL). Several chimeric structures were searched in colonies derived from single cells. All of the structures were found in DNA isolated from each of the colonies. Our findings indicate that interchromosomal rearrangements that generate chimeric chromosomes are recurrent and occur, at a relatively high frequency, in cell populations of S. cerevisiae.

Precise detection of de novo single nucleotide variants in human genomes.

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.

Teleneurology Consultations for Prognostication and Brain Death Diagnosis.

The diagnosis of brain death and the determination of neurologic prognosis following cardiac arrest are important reasons for neurology consultation in the intensive care unit. In hospitals without access to neurology consultation, it may be challenging to address these important questions with high reliability in a timely manner. The American Academy of Neurology has established consensus criteria for diagnosis of brain death, which include (i) comatose state; (ii) presence of apnea; and (iii) absence of brainstem reflexes in the setting of a diagnosis of underlying brain injury compatible with brain death. It has recently been shown that virtual assessment of coma using standardized scales is feasible with good inter-rater reliability. The supervision of apnea testing and the neurologic examination of the brainstem by a remote neurologist are possible if conducted in conjunction with a well-trained and experienced bedside team. In this communication, we explore the essential clinical and legal framework that can support using virtual teleconsultations to address this complex topic.

Impact of Telemedicine in Pediatric Postoperative Care.

Background: A shortage of pediatricians and long wait times in the hospitals render more efficient follow-up visits increasingly important. Virtual visits between physician and patient offer a solution to this problem. Increased awareness, improved technology, and efficient scheduling methods will contribute to the quality and adoption of telemedicine programs. Introduction: The aim of this study was to analyze the impact of pediatric telemedicine on wait times and visit durations, as compared with in-person visits. A secondary goal was to assess the efficiency of different scheduling methods for virtual visits. Materials and Methods: The study included >800 postoperative virtual visits from urology, cardiovascular surgery, and ophthalmology, comprising data on wait times, visit duration, and postvisit satisfaction collected through SBR Health and Redcap. In-person visit data were collected on 14 patients in urology, and satisfaction scores were obtained through Press Ganey for urology and ophthalmology. Results: Patients reported very high satisfaction with virtual visits and benefitted from reduced wait times, while receiving care of comparable duration and quality. Longer blocks of time scheduled exclusively for virtual visits correlated with shorter wait times. Discussion: Supplementing health care with telemedicine is a viable way to provide patient-centered care. Implemented effectively, a telemedicine program can contribute greatly to the value a hospital provides to its patients. Conclusions: Virtual visits provide an efficient way to conduct postoperative visits, reducing wait times and increasing physician efficiency while retaining high satisfaction and quality of care.

Acute modulation of the cholinergic system in the mouse brain detected by pharmacological resting-state functional MRI.

INTRODUCTION: The cholinergic system is involved in learning and memory and is affected in neurodegenerative disorders such as Alzheimer's disease. The possibility of non-invasively detecting alterations of neurotransmitter systems in the mouse brain would greatly improve early diagnosis and treatment strategies. The hypothesis of this study is that acute modulation of the cholinergic system might be reflected as altered functional connectivity (FC) and can be measured using pharmacological resting-state functional MRI (rsfMRI). MATERIAL AND METHODS: Pharmacological rsfMRI was performed on a 9.4T MRI scanner (Bruker BioSpec, Germany) using a gradient echo EPI sequence. All mice were sedated with medetomidine. C57BL/6 mice (N = 15/group) were injected with either saline, the cholinergic antagonist scopolamine, or methyl-scopolamine, after which rsfMRI was acquired. For an additional group (N = 8), rsfMRI scans of the same mouse were acquired first at baseline, then after the administration of scopolamine and finally after the additional injection of the cholinergic agonist milameline. Contextual memory was evaluated with the same setup as the pharmacological rsfMRI using the passive avoidance behavior test. RESULTS: Scopolamine induced a dose-dependent decrease of FC between brain regions involved in memory. Scopolamine-induced FC deficits could be recovered completely by milameline for FC between the hippocampus-thalamus, cingulate-retrosplenial, and visual-retrosplenial cortex. FC between the cingulate-rhinal, cingulate-visual and visual-rhinal cortex could not be completely recovered by milameline. This is consistent with the behavioral outcome, where milameline only partially recovered scopolamine-induced contextual memory deficits. Methyl-scopolamine administered at the same dose as scopolamine did not affect FC in the brain. CONCLUSION: The results of the current study are important for future studies in mouse models of neurodegenerative disorders, where pharmacological rsfMRI may possibly be used as a non-invasive read-out tool to detect alterations of neurotransmitter systems induced by pathology or treatment.

Different anesthesia regimes modulate the functional connectivity outcome in mice.

PURPOSE: The use of resting-state functional MRI (rsfMRI) in preclinical research is expanding progressively, with the majority of resting-state imaging performed in anesthetized animals. Since anesthesia may change the physiology and, in particular, the neuronal activity of an animal considerably, it may also affect rsfMRI findings. Therefore, this study compared rsfMRI data from awake mice with rsfMRI results obtained from mice anesthetized with α-chloralose (120 mg/kg), urethane (2.5 g/kg), or isoflurane (1%). METHODS: Functional connectivity (FC) was estimated using both independent component analysis (40 components) and ROI-based analysis to zoom in on the effect of different anesthetics on inter-hemispheric FC. RESULTS: The data revealed an important diminishment of cortical interhemispheric FC in both the α-chloralose and urethane groups in comparison with the isoflurane and awake groups. CONCLUSION: When performing FC analysis in anesthetized mice, the impact of anesthetics must be taken into account. The required doses for stable anesthesia during MRI significantly decrease interhemispheric FC.

Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs.

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.

A proposal to reduce the amount of permethrin entering wastewater resultant from topical use to treat scabies.

The incidence of scabies is rising in the last years. Subsequently, the use of pharmaceuticals to treat the disease has also increased. Treatment with topical permethrin is usually recommended as a first line agent. This substance is also an aquatic contaminant that is toxic for many non-target organisms, and has been included as a priority substance in the recently published proposal of the European Water Framework Directive. Current guidelines neglect the potential environmental impact of this drug, recommending that the cream should be applied head to toe and "washed off after 8-12 h". Recently, a wiping procedure before hand washing after application of the topical treatment resulted in a 66 % reduction of the amount of diclofenac released in wastewater. The authors suggested that this method could be explored for other topical treatments. In the case of scabiosis, a protocol implicating the whole body needs to be designed. The absorption of topical permethrin is low. Considering the growing incidence of scabies, the amount of the pyrethroid reaching the environment may also be increasing. Therefore, we believe that applying the wiping procedure to the case of topical permethrin deserves consideration. Other measures to minimize the amount of permethrin residues reaching wastewater by washing clothes and bed linen such as wearing single-use pijamas should also be explored. In conclusion, we need to apply a One Health approach in the treatment with scabies, without neglecting the environmental impact of pharmaceuticals. It is not rational to forget drugs once they go down the drain.

Machine Learning-Based Prediction of Changes in the Clinical Condition of Patients With Complex Chronic Diseases: 2-Phase Pilot Prospective Single-Center Observational Study.

BACKGROUND: Functional impairment is one of the most decisive prognostic factors in patients with complex chronic diseases. A more significant functional impairment indicates that the disease is progressing, which requires implementing diagnostic and therapeutic actions that stop the exacerbation of the disease. OBJECTIVE: This study aimed to predict alterations in the clinical condition of patients with complex chronic diseases by predicting the Barthel Index (BI), to assess their clinical and functional status using an artificial intelligence model and data collected through an internet of things mobility device. METHODS: A 2-phase pilot prospective single-center observational study was designed. During both phases, patients were recruited, and a wearable activity tracker was allocated to gather physical activity data. Patients were categorized into class A (BI≤20; total dependence), class B (2060; moderate or mild dependence, or independent). Data preprocessing and machine learning techniques were used to analyze mobility data. A decision tree was used to achieve a robust and interpretable model. To assess the quality of the predictions, several metrics including the mean absolute error, median absolute error, and root mean squared error were considered. Statistical analysis was performed using SPSS and Python for the machine learning modeling. RESULTS: Overall, 90 patients with complex chronic diseases were included: 50 during phase 1 (class A: n=10; class B: n=20; and class C: n=20) and 40 during phase 2 (class B: n=20 and class C: n=20). Most patients (n=85, 94%) had a caregiver. The mean value of the BI was 58.31 (SD 24.5). Concerning mobility aids, 60% (n=52) of patients required no aids, whereas the others required walkers (n=18, 20%), wheelchairs (n=15, 17%), canes (n=4, 7%), and crutches (n=1, 1%). Regarding clinical complexity, 85% (n=76) met patient with polypathology criteria with a mean of 2.7 (SD 1.25) categories, 69% (n=61) met the frailty criteria, and 21% (n=19) met the patients with complex chronic diseases criteria. The most characteristic symptoms were dyspnea (n=73, 82%), chronic pain (n=63, 70%), asthenia (n=62, 68%), and anxiety (n=41, 46%). Polypharmacy was presented in 87% (n=78) of patients. The most important variables for predicting the BI were identified as the maximum step count during evening and morning periods and the absence of a mobility device. The model exhibited consistency in the median prediction error with a median absolute error close to 5 in the training, validation, and production-like test sets. The model accuracy for identifying the BI class was 91%, 88%, and 90% in the training, validation, and test sets, respectively. CONCLUSIONS: Using commercially available mobility recording devices makes it possible to identify different mobility patterns and relate them to functional capacity in patients with polypathology according to the BI without using clinical parameters.

Diffusion kurtosis imaging to detect amyloidosis in an APP/PS1 mouse model for Alzheimer's disease.

PURPOSE: Amyloid deposition in the brain is considered an initial event in the progression of Alzheimer's disease. We hypothesized that the presence of amyloid plaques in the brain of APP/presenilin 1 mice leads to higher diffusion kurtosis measures due to increased microstructural complexity. As such, our purpose was to provide an in vivo proof of principle for detection of amyloidosis by diffusion kurtosis imaging (DKI). METHODS: APPKM670/671NL /presenilin 1 L166P mice (n = 5) and wild-type littermates (n = 5) underwent DKI at the age of 16 months. Averaged diffusion and diffusion kurtosis parameters were obtained for multiple regions (hippocampus-cortex-thalamus-cerebellum). After DKI, mice were sacrificed for amyloid staining. RESULTS: Histograms of the frequency distribution of the DKI parameters tended to shift to higher values. After normalization of absolute values to the cerebellum, a nearly plaque-free region, mean, radial, and axial diffusion kurtosis were significantly higher in APP/presenilin 1 mice as compared to wild-type in the cortex and thalamus, regions demonstrating substantial amyloid staining. CONCLUSION: The current study, although small-scale, suggests increased DKI metrics, in the absence of alterations in diffusion tensor imaging metrics in the cortex and thalamus of APP/presenilin 1 mice with established amyloidosis. These results warrant further investigations on the potential of DKI as a sensitive marker for Alzheimer's disease.

Identification and characterization of Huntington related pathology: an in vivo DKI imaging study.

An important focus of Huntington Disease (HD) research is the identification of symptom-independent biomarkers of HD neuropathology. There is an urgent need for reproducible, sensitive and specific outcome measures, which can be used to track disease onset as well as progression. Neuroimaging studies, in particular diffusion-based MRI methods, are powerful probes for characterizing the effects of disease and aging on tissue microstructure. We report novel diffusional kurtosis imaging (DKI) findings in aged transgenic HD rats. We demonstrate altered diffusion metrics in the (pre)frontal cerebral cortex, external capsule and striatum. Presence of increased diffusion complexity and restriction in the striatum is confirmed by an increased fiber dispersion in this region. Immunostaining of the same specimens reveals decreased number of microglia in the (pre)frontal cortex, and increased numbers of oligodendrocytes in the striatum. We conclude that DKI allows sensitive and specific characterization of altered tissue integrity in this HD rat model, indicating a promising potential for diagnostic imaging of gray and white matter pathology.

The use of antipsychotics in a medium-long stay psychiatric hospital from 1998 to 2010.

OBJECTIVE: Atypical agents have emerged as the dominant choice among antipsychotics. Data about development of antipsychotic use in medium-long stay psychiatric hospitals is lacking. MATERIAL AND METHODS: Antipsychotic drug consumption data and cost was obtained from 1998 to 2010 for all inpatients of a 231-bed psychiatric hospital. Number of hospital stays was obtained from the hospital admission unit. Daily defined dose (DDD) values were those assigned by the WHO. Antipsychotic use was also measured using recently available consensus-based recommendations. Antipsychotic use was then calculated as the sum of individual DDD or total equivalent doses of all antipsychotics divided by the annual stay number. RESULTS: Antipsychotic use increased 135% from 1998 to 2010 when measured in DDDs or 108% when measured with the consensus-based recommendations. Antipsychotic expenditure has risen six-fold since 1998. This augmentation is due to the increase of use of atypical antipsychotics. CONCLUSION: In conclusion, antipsychotic use has at least doubled in the last 13 years. This growth, attributable to an increase in atypical drug use, has contributed to a six-fold increase in the total antipsychotic expenditure. Whether this prescription pattern has translated into palpable clinical benefits remains unclear.

Teleneurology-Enabled Determination of Death by Neurologic Criteria After Cardiac Arrest or Severe Neurologic Injury.

OBJECTIVE: To determine whether providing teleneurology (TN) consultations aiding in determination of death by neurologic criteria (DNC) to a bedside intensivist is feasible and whether timely access and expert input increase the quality of the DNC examination and identification of potential organ donors, we reviewed retrospective data related to outcomes of such consultations. METHODS: Between November 2017 and March 2019, TN consults were requested for sequential comatose patients in the intensive care unit (ICU). We recorded patients' demographic information, causes leading to coma or suspected DNC, and the results of TN consultations. We obtained data on the number of referrals to the organ bank and number of organ donors. RESULTS: Ninety-nine consults were performed with a median time from request to start of the consult of 20.2 minutes (interquartile range 5.4-65.3 minutes). Eighty consults were requested for determination of prognosis, whereas 19 consults were requested for supervision of the DNC examination. In 1 of 80 (1.2%) prognostication consults, the patient was determined by the neurologist to require assessment of DNC and was found to meet DNC criteria; determination of DNC occurred in 11 of the 19 (57.9%) consultations for a supervised DNC examination. In a comparison of the pre-TN (94 months) and post-TN (17 months) periods, there was 2.56-fold increase in the proportion of patients meeting DNC criteria who were medically suitable for donation (pre-TN 8.9% vs post-TN 21.1%, p = 0.02) and a 2.12-fold increase in the proportion of donors (pre-TN 6.14% vs post-TN 13.1%, p = 0.14). CONCLUSIONS: It is feasible to perform TN consultations for patients with severe neurologic damage and to allow expert supervision for DNC examination. Having a teleneurologist as part of the ICU assessment team helped differentiate severe neurologic deficits from DNC and was associated with increase in organ donation.

Identical repeated backbone of the human genome.

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 approximately 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.

Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli.

Strains of the same bacterial species often show considerable genomic variation. To examine the extent of such variation in Rhizobium etli, the complete genome sequence of R. etli CIAT652 and the partial genomic sequences of six additional R. etli strains having different geographical origins were determined. The sequences were compared with each other and with the previously reported genome sequence of R. etli CFN42. DNA sequences common to all strains constituted the greater part of these genomes and were localized in both the chromosome and large plasmids. About 700 to 1,000 kb of DNA that did not match sequences of the complete genomes of strains CIAT652 and CFN42 was unique to each R. etli strain. These sequences were distributed throughout the chromosome as individual genes or chromosomal islands and in plasmids, and they encoded accessory functions, such as transport of sugars and amino acids, or secondary metabolism; they also included mobile elements and hypothetical genes. Sequences corresponding to symbiotic plasmids showed high levels of nucleotide identity (about 98 to 99%), whereas chromosomal sequences and the sequences with matches to other plasmids showed lower levels of identity (on average, about 90 to 95%). We concluded that R. etli has a pangenomic structure with a core genome composed of both chromosomal and plasmid sequences, including a highly conserved symbiotic plasmid, despite the overall genomic divergence.

Genetic characterization of indigenous peoples from Oaxaca, Mexico, and its relation to linguistic and geographic isolation.

We used 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) to genetically characterize 361 individuals from 11 indigenous populations (Amuzgo, Chinanteco, Chontal, Huave, Mazateco, Mixe, Mixteco, Triqui, Zapoteco del Istmo, Zapoteco del Valle, and Zoque) from Oaxaca, Mexico. We also used previously published data from other Mexican peoples (Maya, Chol, Tepehua, Otomí, and Mestizos from northern and central Mexico) to delineate genetic relations, for a total of 541 individuals. Average heterozygosity (H) was lower in most populations from Oaxaca (range 0.687 in Zoque to 0.756 in Chontal) than values observed in Mestizo populations from Mexico (0.758 and 0.793 in central and northern Mestizo, respectively) but higher than values observed in other Amerindian populations from South America; the same relation was true for the number of alleles (n(a) ). We tested (using the software Structure) whether major geographic or linguistic barriers to gene flow existed among the populations of Oaxaca and found that the populations appeared to constitute one or two genetic groups, suggesting that neither geographic location nor linguistics had an effect on the genetic structure of these culturally and linguistically highly diverse indigenous peoples. Moreover, we found a low but statistically significant between-population differentiation. In addition, the genetic structure of Oaxacan populations did not fit an isolation-by-distance model. Finally, using AMOVA and a Bayesian clustering approach, we did not detect significant geographic or linguistic barriers to gene flow within Oaxaca. These results suggest that the indigenous communities of Oaxaca, although culturally isolated, can be genetically defined as a large, nearly panmictic population in which migration could be a more important population mechanism than genetic drift. Finally, compared with outgroups in Mexico (both indigenous peoples and Mestizos), three groups were apparent. Among them, only the Otomí population from Hidalgo has a different culture and language.

Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems.

Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule.