Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans.

Here we studied HLA blocks and haplotypes in a group of 218 Lacandon Maya Native American using a high-resolution next generation sequencing (NGS) method. We assessed the genetic diversity of HLA class I and class II in this population, and determined the most probable ancestry of Lacandon Maya HLA class I and class II haplotypes. Importantly, this Native American group showed a high degree of both HLA homozygosity and linkage disequilibrium across the HLA region and also lower class II HLA allelic diversity than most previously reported populations (including other Native American groups). Distinctive alleles present in the Lacandon population include HLA-A*24:14 and HLA-B*40:08. Furthermore, in Lacandons we observed a high frequency of haplotypes containing the allele HLA-DRB1*04:11, a relatively frequent allele in comparison with other neighboring indigenous groups. The specific demographic history of the Lacandon population including inbreeding, as well as pathogen selection, may have elevated the frequencies of a small number of HLA class II alleles and DNA blocks. To assess the possible role of different selective pressures in determining Native American HLA diversity, we evaluated the relationship between genetic diversity at HLA-A, HLA-B and HLA-DRB1 and pathogen richness for a global dataset and for Native American populations alone. In keeping with previous studies of such relationships we included distance from Africa as a covariate. After correction for multiple comparisons we did not find any significant relationship between pathogen diversity and HLA genetic diversity (as measured by polymorphism information content) in either our global dataset or the Native American subset of the dataset. We found the expected negative relationship between genetic diversity and distance from Africa in the global dataset, but no relationship between HLA genetic diversity and distance from Africa when Native American populations were considered alone

Statistically coherent calibration of X-Ray Fluorescence Spectrometry for major elements in rocks in minerals.

We applied both the ordinary linear regression (OLR) and the new uncertainty weighted linear regression (UWLR) models for the calibration and comparison of a XRF machine through 59 geochemical reference materials (GRMs) and a procedure blank sample. )e mean concentration and uncertainty data for the GRMs used for the calibrations (Supplementary Materials) (available here) filewere achieved from an up-to-date compilation of chemical data and their processing from well-known discordancy and significance tests. )e drift-corrected XRF intensity and its uncertainty were determined from mostly duplicate pressed powder pellets. )e comparison of the OLR (linear correlation coefficient r∼0.9523–0.9964 and 0.9771–0.9999, respectively, for before and after matrix correction) and UWLR models (r∼0.9772–0.9976 and 0.9970–0.9999, respectively) clearly showed that the latter with generally higher values of r is preferable for routine calibrations of analytical procedures. Both calibrations were successfully applied to rock matrices, and the results were generally consistent with those obtained in other laboratories although the UWLR model showed mostly narrower confidence limits of the mean (slope and intercept) or lower uncertainties than the OLR. Similar sensitivity (∼2.69–46.17 kc·s1·%1 for the OLR and ∼2.78–59.69 kc·s1·%1 for the UWLR) also indicated that the UWLR could advantageously replace the OLR model. Another novel aspect is that the total uncertainty can be reported for individual chemical data. If the analytical instruments were routinely calibrated from the UWLR model, this action would make the science of geochemistry more quantitative than at present

Characterization of the fetal membranes in buffalo cows in the first three months of gestation

Este estudo visou à caracterização das membranas fetais em búfalas (Bubalus bubalis, Linnaeus 1758) no terço inicial da gestação. As membranas fetais foram analisadas macroscópica e microscopicamente (luz e microscopia eletrônica de transmissão). O córion possui uma camada simples de células circulares, com núcleos de forma esférica, denominadas trofobláticas; há outro tipo celular, as células trofoblásticas gigantes, com dois ou mais núcleos. Ambas possuem uma grande quantidade de vesículas no citoplasma e retículo endoplasmático à microscopia de transmissão. O alantóide possui vasos preenchidos com eritrócitos, e contêm células alongadas, que formam um epitélio estratificado simples. O âmnion é uma membrana transparente, ou esbranquiçada; constituído por epitélio estratificado simples. A diferença principal entre o alantóide e o âmnion é que o último é avascular. O saco vitelínico é uma membrana opaca que desaparece durante a gestação; é a única membrana que não está em contato com as outras e apresenta três tipos diferentes de células que dão forma a três camadas distintas (endoderma, mesotélio, mesênquima)The aim of the study was to characterize the fetal membranes in buffalo cows (Bubalus bubalis, Linnaeus 1758) in the first 3 months of the gestation. The fetal membranes were analyzed gross and microscopically (light and ultrastructural analysis). The corion is a simple layer of circle cells, with spherical nucleus, named trofoblastics; there is another cellular type, named trophoblastic giant cells, with two or more nucleus. Both of them have many cytoplasmic and reticule endoplasmic vesicles on transmission electron microscopy. The allantoic has many vessels filled with eritrocytes, elongated cells which form a stratified simple epithelium. The amnion is transparent or sometimes whitish, consisting of a stratified simple epithelium. The main difference between the allantoic and amnion is that the latter is avascular. The yolk sac is an opaque membrane that disappears during gestation, and is the only membrane that is not in contact with the others; it presents three different types of cells which form three distinct layers (endoderm, mesothelium and mesenquimal

Accommodating a Non-Conservative Internal Mutation by WaterMediated Hydrogen-Bonding Between β-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b5

Mammalian type B (mitochondrial) cytochromes b5 exhibit greater amino acid sequence diversity than their type A (microsomal) counterparts, as exemplified by the type B proteins from human (hCYB5B) and rat (rCYB5B). The comparison of X-ray crystal structures of hCYB5B and rCYB5B reported herein reveals a striking difference in packing involving the five-stranded β-sheet, attributable to fully buried residue 21 in strand β4. The greater bulk of Leu21 in hCYB5B in comparison to Thr21 in rCYB5B results in a substantial displacement of the first two residues in β5, and consequent loss of two of the three hydrogen bonds between β5 and β4. Hydrogen-bonding between the residues is instead mediated by two well-ordered, fully buried water molecules. In a 10 ns molecular dynamics simulation, one of the buried water molecules in the hCYB5B structure exchanged readily with solvent via intermediates having three water molecules sandwiched between β4 and β5. When the buried water molecules were removed prior to a second 10 ns simulation, β4 and β5 formed persistent hydrogen bonds identical to those in rCYB5B, but the Leu21 side chain was forced to adopt a rarely observed conformation. Despite the apparently greater ease of water access to the interior of hCYB5B than of rCYB5B suggested by these observations, the two proteins exhibit virtually identical stability, dynamic and redox properties. The results provide new insight into the factors stabilizing the cytochrome b5 fold

Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science

“The most dangerous phrase in the language is: We’ve always done it this way.” —Rear Admiral Grace HopperSuccess and impact metrics in science are based on a system that perpetuates sexist and racist “rewards” by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals’ meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change.Peer reviewe

The 2021 EULAR/American College of Rheumatology points to consider for diagnosis, management and monitoring of the interleukin-1 mediated autoinflammatory diseases: cryopyrin-associated periodic syndromes, tumour necrosis factor receptor-associated periodic syndrome, mevalonate kinase deficiency, and deficiency of the interleukin-1 receptor antagonist

BACKGROUND: The interleukin-1 (IL-1) mediated systemic autoinflammatory diseases, including the cryopyrin-associated periodic syndromes (CAPS), tumour necrosis factor receptor-associated periodic syndrome (TRAPS), mevalonate kinase deficiency (MKD) and deficiency of the IL-1 receptor antagonist (DIRA), belong to a group of rare immunodysregulatory diseases that primarily present in early childhood with variable multiorgan involvement. When untreated, patients with severe clinical phenotypes have a poor prognosis, and diagnosis and management of these patients can be challenging. However, approved treatments targeting the proinflammatory cytokine IL-1 have been life changing and have significantly improved patient outcomes. OBJECTIVE: To establish evidence-based recommendations for diagnosis, treatment and monitoring of patients with IL-1 mediated autoinflammatory diseases to standardise their management. METHODS: A multinational, multidisciplinary task force consisting of physician experts, including rheumatologists, patients or caregivers and allied healthcare professionals, was established. Evidence synthesis, including systematic literature review and expert consensus (Delphi) via surveys, was conducted. Consensus methodology was used to formulate and vote on statements to guide optimal patient care. RESULTS: The task force devised five overarching principles, 14 statements related to diagnosis, 10 on therapy, and nine focused on long-term monitoring that were evidence and/or consensus-based for patients with IL-1 mediated diseases. An outline was developed for disease-specific monitoring of inflammation-induced organ damage progression and reported treatments of CAPS, TRAPS, MKD and DIRA. CONCLUSION: The 2021 EULAR/American College of Rheumatology points to consider represent state-of-the-art knowledge based on published data and expert opinion to guide diagnostic evaluation, treatment and monitoring of patients with CAPS, TRAPS, MKD and DIRA, and to standardise and improve care, quality of life and disease outcomes

The 2021 EULAR/American College of Rheumatology Points to Consider for Diagnosis, Management and Monitoring of the Interleukin-1 Mediated Autoinflammatory Diseases: Cryopyrin-Associated Periodic Syndromes, Tumour Necrosis Factor Receptor-Associated Periodic Syndrome, Mevalonate Kinase Deficiency, and Deficiency of the Interleukin-1 Receptor Antagonist

BACKGROUND: The interleukin-1 (IL-1) mediated systemic autoinflammatory diseases, including the cryopyrin- associated periodic syndromes (CAPS), tumour necrosis factor receptor-associated periodic syndrome (TRAPS), mevalonate kinase deficiency (MKD) and deficiency of the IL-1 receptor antagonist (DIRA), belong to a group of rare immunodysregulatory diseases that primarily present in early childhood with variable multiorgan involvement. When untreated, patients with severe clinical phenotypes have a poor prognosis, and diagnosis and management of these patients can be challenging. However, approved treatments targeting the proinflammatory cytokine IL-1 have been life changing and have significantly improved patient outcomes. OBJECTIVE: To establish evidence-based recommendations for diagnosis, treatment and monitoring of patients with IL-1 mediated autoinflammatory diseases to standardise their management. METHODS: A multinational, multidisciplinary task force consisting of physician experts, including rheumatologists, patients or caregivers and allied healthcare professionals, was established. Evidence synthesis, including systematic literature review and expert consensus (Delphi) via surveys, was conducted. Consensus methodology was used to formulate and vote on statements to guide optimal patient care. RESULTS: The task force devised five overarching principles, 14 statements related to diagnosis, 10 on therapy, and nine focused on long-term monitoring that were evidence and/or consensus-based for patients with IL-1 mediated diseases. An outline was developed for disease-specific monitoring of inflammation-induced organ damage progression and reported treatments of CAPS, TRAPS, MKD and DIRA. CONCLUSION: The 2021 EULAR/American College of Rheumatology points to consider represent state-of-the-art knowledge based on published data and expert opinion to guide diagnostic evaluation, treatment and monitoring of patients with CAPS, TRAPS, MKD and DIRA, and to standardise and improve care, quality of life and disease outcomes

Primera aproximación al uso de la ocupación del tapir (Tapirella bairdii Gill, 1865) como indicador de la integridad ecológica en la Reserva de la Biosfera Maya, Guatemala

La Reserva de la Biosfera Maya (RBM) es un área protegida de relevancia nacional, regional y mundial por la diversidad biológica  asociada  y  los  beneficios  que  se  obtienen  de  esta.  En  su  plan  maestro  se  plantea  el  conjunto  de  elementos  de conservación a partir de los cuales se orientan estrategias y se evalúa la efectividad de manejo de dicha reserva, entre los cuales se incluye a Tapirella  bairdii  (tapir), por lo que es importante contar con un monitoreo de esta especie como una  herramienta para la administración de esta reserva. En el 2015 se inició el desarrollo de un protocolo de monitoreo basado en la estimación de  la  probabilidad de  ocupación  y el  presente  estudio constituye  la  continuación de  esta  iniciativa  a  través de la implementación de las  temporadas  de muestreo en 2017 y 2018. Se registró la presencia del tapir en cinco zonas núcleo de la RBM empleando trampas cámara y se estimó la probabilidad de ocupación. Los valores estimados sugieren una relación  de la ocupación con la integridad ecológica, en la cual hay una mayor ocupación en áreas con menor perturbación. Se generaron modelos con cinco covariables relacionadas con amenazas potenciales, sin embargo fue el modelo nulo el que se  seleccionó  de  acuerdo  al  criterio  definido.  Los  resultados  sugieren  que  la  integridad  ecológica  en  las  áreas  de  estudio  está siendo afectada  como consecuencia  de  las presiones antrópicas por lo que  es necesario el  fortalecimiento de  aquellas con menores valores de ocupación.

De Novo Unbalanced Translocations in Prader-Willi and Angelman Syndrome Might Be the Reciprocal Product of inv dup(15)s

The 15q11-q13 region is characterized by high instability, caused by the presence of several paralogous segmental duplications. Although most mechanisms dealing with cryptic deletions and amplifications have been at least partly characterized, little is known about the rare translocations involving this region. We characterized at the molecular level five unbalanced translocations, including a jumping one, having most of 15q transposed to the end of another chromosome, whereas the der(15)(pter->q11-q13) was missing. Imbalances were associated either with Prader-Willi or Angelman syndrome. Array-CGH demonstrated the absence of any copy number changes in the recipient chromosome in three cases, while one carried a cryptic terminal deletion and another a large terminal deletion, already diagnosed by classical cytogenetics. We cloned the breakpoint junctions in two cases, whereas cloning was impaired by complex regional genomic architecture and mosaicism in the others. Our results strongly indicate that some of our translocations originated through a prezygotic/postzygotic two-hit mechanism starting with the formation of an acentric 15qter->q1::q1->qter representing the reciprocal product of the inv dup(15) supernumerary marker chromosome. An embryo with such an acentric chromosome plus a normal chromosome 15 inherited from the other parent could survive only if partial trisomy 15 rescue would occur through elimination of part of the acentric chromosome, stabilization of the remaining portion with telomere capture, and formation of a derivative chromosome. All these events likely do not happen concurrently in a single cell but are rather the result of successive stabilization attempts occurring in different cells of which only the fittest will finally survive. Accordingly, jumping translocations might represent successful rescue attempts in different cells rather than transfer of the same 15q portion to different chromosomes. We also hypothesize that neocentromerization of the original acentric chromosome during early embryogenesis may be required to avoid its loss before cell survival is finally assured

2019 Scholars at Work Conference Program

Program for the 2019 Scholars at Work Conference at Minnesota State University, Mankato on March 29, 2019