Latiné immigrant heterogeneity: Striking health differences among Cuban refugee/migration waves to the United States.

Latiné people differ markedly in our lived experiences in ways that are underappreciated. Meanwhile, variations in social experiences are known to be associated with differential health outcomes. We test whether immigration history is associated with health differences among U.S.-based Cuban refugees. Cubans from the circum-1980 Mariel Boatlift migration wave reported significantly higher instances of disability than Early Cuban Exiles, Freedom Flight refugees, and Special Period refugees. We also interviewed Miami-based Cubans. Participants described heightened discrimination in 1980s Cuba and U.S., which we hypothesize contributed to higher instances of disability refugees of that era. By understanding how differential social experiences shape health, we aim to provide a nuanced understanding of the social determinants of health and the ways adverse experiences can be combated.

Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life.

Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabacterium at the genomic level, we sequenced and analyzed 25 genomes from Australian soil-burrowing cockroaches (Blaberidae: Panesthiinae), which have undergone at least seven separate subterranean, subsocial transitions from above-ground, wood-feeding ancestors. We find at least three independent instances of genome erosion have occurred in Blattabacterium strains exclusive to Australian soil-burrowing cockroaches. These shrinkages have involved the repeated inactivation of genes involved in amino acid biosynthesis and nitrogen recycling, the core role of Blattabacterium in the host-symbiont relationship. The most drastic of these erosions have occurred in hosts thought to have transitioned underground the earliest relative to other lineages, further suggestive of a link between gene loss in Blattabacterium and the burrowing behavior of hosts. As Blattabacterium is unable to fulfill its core function in certain host lineages, these findings suggest soil-burrowing cockroaches must acquire these nutrients from novel sources. Our study represents one of the first cases, to our knowledge, of parallel host adaptations leading to concomitant parallelism in their mutualistic symbionts, further underscoring the intimate relationship between these two partners.

Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles.

Chemical cues in subterranean habitats differ highly from those on the surface due to the contrasting environmental conditions, such as absolute darkness, high humidity or food scarcity. Subterranean animals underwent changes to their sensory systems to facilitate the perception of essential stimuli for underground lifestyles. Despite representing unique systems to understand biological adaptation, the genomic basis of chemosensation across cave-dwelling species remains unexplored from a macroevolutionary perspective. Here, we explore the evolution of chemoreception in three beetle tribes that underwent at least six independent transitions to the underground, through a phylogenomics spyglass. Our findings suggest that the chemosensory gene repertoire varies dramatically between species. Overall, no parallel changes in the net rate of evolution of chemosensory gene families were detected prior, during, or after the habitat shift among subterranean lineages. Contrarily, we found evidence of lineage-specific changes within surface and subterranean lineages. However, our results reveal key duplications and losses shared between some of the lineages transitioning to the underground, including the loss of sugar receptors and gene duplications of the highly conserved ionotropic receptors IR25a and IR8a, involved in thermal and humidity sensing among other olfactory roles in insects. These duplications were detected both in independent subterranean lineages and their surface relatives, suggesting parallel evolution of these genes across lineages giving rise to cave-dwelling species. Overall, our results shed light on the genomic basis of chemoreception in subterranean beetles and contribute to our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.

Short Sequence Aligner Benchmarking for Chromatin Research.

Much of today's molecular science revolves around next-generation sequencing. Frequently, the first step in analyzing such data is aligning sequencing reads to a reference genome. This step is often taken for granted, but any analysis downstream of the alignment will be affected by the aligner's ability to correctly map sequences. In most cases, for research into chromatin structure and nucleosome positioning, ATAC-seq, ChIP-seq, and MNase-seq experiments use short read lengths. How well aligners manage these reads is critical. Most aligner programs will output mapped reads and unmapped reads. However, from a biological point of view, reads will fall into one of three categories: correctly mapped, incorrectly mapped, and unmapped. While increased sequencing depth can often compensate for unmapped reads, incorrectly and correctly mapped reads appear algorithmically identical but can produce biologically significant alterations in the results. For this reason, we are benchmarking various alignment programs to determine their propensity to incorrectly map short reads. As short-read alignment is an important step in ATAC-seq, ChIP-seq, and MNase-seq experiments, caution should be taken in mapping reads to ensure that the most accurate conclusions can be made from the data generated. Our analysis is intended to help investigators new to the field pick the alignment program best suited for their experimental conditions. In general, the aligners we tested performed well. BWA, Bowtie2, and Chromap were all exceptionally accurate, and we recommend using them. Furthermore, we show that longer read lengths do in fact lead to more accurate mappings.

Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.

Computer programming is a fundamental tool for life scientists, allowing them to carry out essential research tasks. However, despite various educational efforts, learning to write code can be a challenging endeavor for students and researchers in life-sciences disciplines. Recent advances in artificial intelligence have made it possible to translate human-language prompts to functional code, raising questions about whether these technologies can aid (or replace) life scientists' efforts to write code. Using 184 programming exercises from an introductory-bioinformatics course, we evaluated the extent to which one such tool-OpenAI's ChatGPT-could successfully complete programming tasks. ChatGPT solved 139 (75.5%) of the exercises on its first attempt. For the remaining exercises, we provided natural-language feedback to the model, prompting it to try different approaches. Within 7 or fewer attempts, ChatGPT solved 179 (97.3%) of the exercises. These findings have implications for life-sciences education and research. Instructors may need to adapt their pedagogical approaches and assessment techniques to account for these new capabilities that are available to the general public. For some programming tasks, researchers may be able to work in collaboration with machine-learning models to produce functional code.

Parallel and convergent genomic changes underlie independent subterranean colonization across beetles.

Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna.

Multidimensional separation methods for in-depth proteome profiling of low-microgram samples.

Tweetable abstract Multidimensional separation methods with improved sensitivity and peak capacity and throughput allow in-depth proteome profiling of low-microgram samples.

Influence of preovulatory estradiol treatment on the maintenance of pregnancy in beef cattle receiving in vivo produced embryos.

This experiment was designed to determine the role of preovulatory estradiol in pregnancy retention after embryo transfer (ET). Cows were synchronized with the 7-d CO-Synch + CIDR® protocol. On d0 (d-2 =CIDR® removal), cows were grouped by estrual status (estrual [Positive Control] and nonestrual), and nonestrual cows were administered Gonadotropin Releasing Hormone (GnRH) and randomly assigned to either no treatment (Negative Control) or Estradiol (0.1 mg estradiol 17-ß IM). All cows received an embryo on d7. Pregnancy status was retrospectively classified on d56, 30, 24, and 19 by either ultrasonography, plasma pregnancy-associated glycoproteins analysis (PAGs), expression of interferon-stimulated genes, plasma progesterone (P4) concentrations, or a combination of the factors. There was no difference in estradiol concentrations on day 0 h 0 (P > 0.16). At day 0 h 2, Estradiol cows (15.7 ± 0.25 pg/mL) had elevated (P < 0.001) estradiol compared with Positive Controls (3.4 ± 0.26 pg/mL) or Negative Controls (4.3 ± 0.25 pg/mL). On d19, pregnancy rates did not differ (P = 0.14) among treatments. On d24, Positive Controls (47%) had greater (P < 0.01) pregnancy rates than Negative Controls (32%); Estradiol cows were intermediate (40%). There was no difference (P = 0.38) in pregnancy rates between Positive Control (41%) and Estradiol (36%) cows on d30, but Negative Control (27%) cows had (P = 0.01) or tended (P = 0.08) to have decreased pregnancy rates, respectively. Thus, preovulatory estradiol may elicit an effect on early uterine attachment or alter histotroph components, consequently improving pregnancy maintenance through d30.

Timing and duration of nutrient restriction and its impacts on placental development and umbilical blood flow in adolescent sheep.

We hypothesized that nutrient restriction from day 50-90 of gestation decreases umbilical blood flow and that umbilical blood flow would recover to control values upon realimentation during late gestation (d 90 to 130) or remain reduced in ewes that continued to be nutrient restricted. On d 50 of gestation, young nulliparous whiteface ewes (6-8 mo; n = 41) carrying singletons were randomly assigned to two dietary treatments: 100% of NRC recommendations (CON) or 60% of CON (RES). On d 90 of gestation, ewes either remained on CON or RES until d 130, or CON ewes were RES from d 90 to 130, or RES ewes were realimented to CON from d 90 to 130. This resulted in 4 treatment groups on day 130: CON-CON, CON-RES, RES-RES, RES-CON. Umbilical blood flow and fetal and placental measurements were obtained via ultrasonography every 10 days from day 50-110. Non-survival surgeries were performed on days 50, 90, and 130 (n = 6-7 ewes/group) where uterine artery and umbilical blood flows were measured during surgery via ultrasonography. Conceptus weights were recorded and placentomes collected to determine binucleate cell numbers. The study was conducted as a completely randomized design arrangement with repeated measures. Data were analyzed using the MIXED procedure of SAS. There was a nutritional treatment by day interaction (P < 0.01) with CON ewes having greater umbilical blood flow compared with RES by d 90. Fetal biparietal distance, abdominal width, and kidney area increased (P < 0.05) in CON-RES with all these measurements increasing during late gestation. We partially accept our hypothesis as nutrient restriction during mid gestation decreased umbilical blood flow. However, blood flow did not return to control levels upon realimentation. By d 130, fetal and placental weights were similar between RES-RES and CON-CON. Binucleate cell numbers in the fetal trophoblast were not influenced by nutritional treatments. Our findings suggest that refeeding previously nutrient restricted pregnant adolescent ewes to control levels does not reestablish umbilical blood flow. Adequate placental development during mid gestation could protect the fetus from a decreased umbilical blood flow later in gestation when nutrients were limited by 40%.

Tracking B Cell Memory to SARS-CoV-2 Using Rare Cell Analysis System.

Rapid mutations within SARS-CoV-2 are driving immune escape, highlighting the need for in-depth and routine analysis of memory B cells (MBCs) to complement the important but limited information from neutralizing antibody (nAb) studies. In this study, we collected plasma samples and peripheral blood mononuclear cells (PBMCs) from 35 subjects and studied the nAb titers and the number of antigen-specific memory B cells at designated time points before and after vaccination. We developed an assay to use the MiSelect R II System with a single-use microfluidic chip to directly detect the number of spike-receptor-binding domain (RBD)-specific MBCs in PBMCs. Our results show that the number of spike-RBD-specific MBCs detected by the MiSelect R II System is highly correlated with the level of nAbs secreted by stimulated PBMCs, even 6 months after vaccination when nAbs were generally not present in plasma. We also found antigen-specific cells recognizing Omicron spike-RBD were present in PBMCs from booster vaccination of subjects, but with a high variability in the number of B cells. The MiSelect R II System provided a direct, automated, and quantitative method to isolate and analyze subsets of rare cells for tracking cellular immunity in the context of a rapidly mutating virus.

High-resolution mass spectrometry for glycoproteomics.

Tweetable abstract Bottom-up glycoproteomics combined with top-down strategy allows direct analysis of glycoform-mapped glycosylation and its glycans by high-resolution mass spectrometry.

Genetic risk for schizophrenia is associated with increased proportion of indirect connections in brain networks revealed by a semi-metric analysis: evidence from population sample stratified for polygenic risk.

Research studies based on tractography have revealed a prominent reduction of asymmetry in some key white-matter tracts in schizophrenia (SCZ). However, we know little about the influence of common genetic risk factors for SCZ on the efficiency of routing on structural brain networks (SBNs). Here, we use a novel recall-by-genotype approach, where we sample young adults from a population-based cohort (ALSPAC:N genotyped = 8,365) based on their burden of common SCZ risk alleles as defined by polygenic risk score (PRS). We compared 181 individuals at extremes of low (N = 91) or high (N = 90) SCZ-PRS under a robust diffusion MRI-based graph theoretical SBN framework. We applied a semi-metric analysis revealing higher SMR values for the high SCZ-PRS group compared with the low SCZ-PRS group in the left hemisphere. Furthermore, a hemispheric asymmetry index showed a higher leftward preponderance of indirect connections for the high SCZ-PRS group compared with the low SCZ-PRS group (PFDR < 0.05). These findings might indicate less efficient structural connectivity in the higher genetic risk group. This is the first study in a population-based sample that reveals differences in the efficiency of SBNs associated with common genetic risk variants for SCZ.

Recent development in hydrophilic interaction liquid chromatography stationary materials for glycopeptide analysis.

Protein glycosylation is one of the most important post-translational modifications, and aberrant glycosylation is associated with the occurrence and development of diseases. Deciphering abnormal glycosylation changes can identify disease-specific signatures to facilitate the discovery of potential disease biomarkers. However, glycosylation analysis is challenging due to the diversity of glycans, heterogeneity of glycosites, and poor electrospray ionization of mass spectrometry. To overcome these obstacles, glycosylation is often elucidated using enriched glycopeptides by removing highly abundant non-glycopeptides. Hydrophilic interaction liquid chromatography (HILIC) is widely used for glycopeptide enrichment due to its excellent selectivity and specificity to hydrophilic glycans and compatibility with mass spectrometry. However, the development of HILIC has lagged far behind hydrophobic interaction chromatography, so efforts to further improve the performance of HILIC are beneficial for glycosylation analysis. This review discusses recent developments in HILIC materials and their advanced applications. Based on the physiochemical properties of glycopeptides, the use of amino acids or peptides as stationary phases showed improved enrichment and separation of glycopeptides. We can envision that the use of glycopeptides as stationary phases would definitely further improve the selectivity and specificity of HILIC for glycosylation analysis.

Differential transcriptomic responses to heat stress in surface and subterranean diving beetles.

Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CTmax 38 °C cf. 42-46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35 °C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response; these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.

Advances in glycopeptide enrichment methods for the analysis of protein glycosylation over the past decade.

Advances in bioanalytical technology have accelerated the analysis of complex protein glycosylation, which is beneficial to understand glycosylation in drug discovery and disease diagnosis. Due to its biological uniqueness in the course of disease occurrence and development, disease-specific glycosylation requires quantitative characterization of protein glycosylation. We provide a comprehensive review of recent advances in glycosylation analysis, including workflows for glycoprotein digestion, glycopeptide separation and enrichment, and mass spectrometry sequencing. We specifically focus on different strategies for glycopeptide enrichment through physical interaction, chemical oxidation, or metabolic labeling of intact glycopeptides. Recent advances and challenges of O-glycosylation analysis are presented, and the development of improved enrichment methods combining different proteases to analyze O-glycosylation is also proposed.

The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.

Ramp sequences occur when the average translational efficiency of codons near the 5' end of highly expressed genes is significantly lower than the rest of the gene sequence, which counterintuitively increases translational efficiency by decreasing downstream ribosomal collisions. Here, we show that the relative codon adaptiveness within different tissues changes the existence of a ramp sequence without altering the underlying genetic code. We present the first comprehensive analysis of tissue and cell type-specific ramp sequences and report 3108 genes with ramp sequences that change between tissues and cell types, which corresponds with increased gene expression within those tissues and cells. The Ramp Atlas (https://ramps.byu.edu/) allows researchers to query precomputed ramp sequences in 18 388 genes across 62 tissues and 66 cell types and calculate tissue-specific ramp sequences from user-uploaded FASTA files through an intuitive web interface. We used The Ramp Atlas to identify seven SARS-CoV-2 genes and seven human SARS-CoV-2 entry factor genes with tissue-specific ramp sequences that may help explain viral proliferation within those tissues. We anticipate that The Ramp Atlas will facilitate personalized and creative tissue-specific ramp sequence analyses for both human and viral genes that will increase our ability to utilize this often-overlooked regulatory region.

Parallel decay of vision genes in subterranean water beetles.

In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.

RNA sequencing and iTRAQ proteomic data from an experiment examining the influence of conceptus presence and preovulatory estradiol on endometrial gene transcripts and proteins around maternal recognition of pregnancy in beef cattle.

RNA sequencing reads and isobaric tags for a relative and absolute quantification (iTRAQ)-Based Proteomic Data were used to determine the impact of conceptus presence and preovulatory estradiol concentration on function of the d16 uterus in beef cattle. Conceptuses and endometrial biopsies were collected from the uterine horn ipsilateral to the corpus luteum. Total cellular RNA was extracted from endometrium for RNA sequencing across two lanes of a NovaSeq S2, 2 × 50-bp run. Two independent uterine luminal fluid pools (ULF) were made for each group: highE2/conceptus, highE2/noconceptus, lowE2/conceptus, and lowE2/noconceptus. Peptides were labeled with iTRAQ reagents and analyzed using 2-dimensional liquid chromatography mass spectrometry. Transcript abundances were determined using DESeq2 (FDR <0.05, FC>2). Scaffold Q+ was used to quantitate peptide and protein identifications in ULF. Datasets include uterine transcript and protein abundances among highE2/conceptus vs highE2/noconceptus and lowE2/conceptus vs lowE2/noconceptus groups. This information can be useful for further investigating the role of specific transcripts and proteins in the maintenance of early pregnancy in beef cattle. This dataset is related to the article 'Influence of conceptus presence and preovulatory estradiol exposure on uterine gene transcripts and proteins around maternal recognition of pregnancy in beef cattle' by E.J. Northrop-Albrecht, J.J.J. Rich, R.A. Cushman, R. Yao, X. Ge, G.A. Perry. Molecular and Cellular Endocrinology.