Search

The common murre (Uria aalge) is a species of seabird particularly vulnerable to several environmental stressors, including parasitic infection and oil contamination. However, the molecular response to these stressors is severely understudied. This study investigated the common murre's transcriptomic responses to these stressors. Blood samples were collected from common murres undergoing rehabilitation at International Bird Rescue in Fairfield, CA. Total RNA was extracted from these samples, followed by library preparation and Illumina sequencing to generate whole transcriptome data. Differential gene expression analysis was conducted using DeSeq2 to identify genes significantly altered in response to oil contamination and parasitic infection. Differential gene expression analysis revealed 194 genes shared between oil-contaminated and infected birds, including key immune-related genes, such as ANXA2, LY96, and LY86. These genes play vital roles inmediating the production of pro-inflammatory cytokines. Gene Set Enrichment Analysis indicated significant alterations in stress, immune, and inflammatory responses, with additional lipid metabolism changes in contaminated birds. Our findings highlight the detrimental effects that these stressors have on wild birds. These findings suggest a generalized stress response and specific metabolic adaptations to oil exposure, providing insights for seabird conservation. [ABSTRACT FROM AUTHOR]

Instructor Talk--noncontent language used by instructors in classrooms--is a recently defined and promising variable for better understanding classroom dynamics. Having previously characterized the Instructor Talk framework within the context of a single course, we present here our results surrounding the applicability of the Instructor Talk framework to noncontent language used by instructors in novel course contexts. We analyzed Instructor Talk in eight additional biology courses in their entirety and in 61 biology courses using an emergent sampling strategy. We observed widespread use of Instructor Talk with variation in the amount and category type used. The vast majority of Instructor Talk could be characterized using the originally published Instructor Talk framework, suggesting the robustness of this framework. Additionally, a new form of Instructor Talk--Negatively Phrased Instructor Talk, language that may discourage students or distract from the learning process--was detected in these novel course contexts. Finally, the emergent sampling strategy described here may allow investigation of Instructor Talk in even larger numbers of courses across institutions and disciplines. Given its widespread use, potential influence on students in learning environments, and ability to be sampled, Instructor Talk may be a key variable to consider in future research on teaching and learning in higher education.

The soil moisture active passive (SMAP) microwave radiometer is a fully-polarimetric L-band radiometer flown on the SMAP satellite in a 6 AM /6 PM sun-synchronous orbit at 685-km altitude. After the SMAP L1B_TB data product version 4 was released in 2018, the radiometer has undergone further calibration and validation. The goal is to reduce the difference between antenna temperature of ascending and descending orbits during the eclipse, and to reduce the dips in the calibration drift over the cold sky (CS) during the eclipse seasons in 2017 and 2018. The postlaunch calibration algorithm has been revisited by retrieving all of the calibration parameters simultaneously with two different options for the hot calibration source (the global ocean, or the radiometer internal reference load). The performance of the two options are compared here. The option with the radiometer internal reference load has been chosen by the SMAP science team for data release version 5. In addition, a correction offset is applied to the input signal to account for offsets during the early-mission stages with the SMAP synthetic aperture radar transmitter operating alongside the radiometer.

Many efforts to improve science teaching in higher education focus on a few faculty members at an institution at a time, with limited published evidence on attempts to engage faculty across entire departments. We created a long-term, department-wide collaborative professional development program, Biology Faculty Explorations in Scientific Teaching (Biology FEST). Across 3 years of Biology FEST, 89% of the department's faculty completed a weeklong scientific teaching institute, and 83% of eligible instructors participated in additional semester-long follow-up programs. A semester after institute completion, the majority of Biology FEST alumni reported adding active learning to their courses. These instructor self-reports were corroborated by audio analysis of classroom noise and surveys of students in biology courses on the frequency of active-learning techniques used in classes taught by Biology FEST alumni and nonalumni. Three years after Biology FEST launched, faculty participants overwhelmingly reported that their teaching was positively affected. Unexpectedly, most respondents also believed that they had improved relationships with departmental colleagues and felt a greater sense of belonging to the department. Overall, our results indicate that biology department-wide collaborative efforts to develop scientific teaching skills can indeed attract large numbers of faculty, spark widespread change in teaching practices, and improve departmental relations.

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution. [ABSTRACT FROM AUTHOR]

Abstract Background Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility. Methods We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold. Results We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome. Conclusions Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.

The creeping vole Microtus oregoni exhibits remarkably transformed sex chromosome biology, with complete chromosome drive/drag, X‐Y fusions, sex reversed X complements, biased X inactivation, and X chromosome degradation. Beginning with a selfish X chromosome, I propose a series of adaptations leading to this system, each compensating for deleterious consequences of the preceding adaptation: (1) YY embryonic inviability favored evolution of a selfish feminizing X chromosome; (2) the consequent Y chromosome transmission disadvantage favored X‐Y fusion ("XP"); (3) Xist‐based silencing of Y‐derived XP genes favored a second X‐Y fusion ("XM"); (4) X chromosome dosage‐related costs in XPXM males favored the evolution of XM loss during spermatogenesis; (5) X chromosomal dosage‐related costs in XM0 females favored the evolution of XM drive during oogenesis; and (6) degradation of the non‐recombining XP favored the evolution of biased X chromosome inactivation. I discuss recurrent rodent sex chromosome transformation, and selfish genes as a constructive force in evolution. [ABSTRACT FROM AUTHOR]

Since their initial development in the early 2000s, institutional repositories (IRs) have proliferated around the globe. Due to low faculty participation, however, content recruitment has often posed a significant challenge for librarians and others promoting their use. Through the last decade, academic social networks (ASNs), such as ResearchGate and Academia.edu, have become popular among scholars as a means to communicate with each other and share their research. Semi-structured interviews were conducted with sixty scholars at six universities in Canada and South Africa to explore their views and practices pertaining to IRs and ASNs. Interviews were transcribed and coded to elucidate trends and themes in the data. The study found that few participants were active supporters of their local IRs. Lack of awareness, time limitations, and concerns regarding copyright remain some of the main obstacles to increased faculty participation. Conversely, more than half of the interviewees were active users of either ResearchGate or Academia.edu. These users valued ASNs both as a means of sharing their work and as tools facilitating connections with their colleagues internationally. Though IRs need not compete with these networks, proponents of open access repositories should be prepared to explain to faculty why they should consider having their research made accessible in a repository though they may already actively share their work through ResearchGate or Academia.edu. Significantly, both ASNs and IRs were more popular among South African than Canadian researchers. It is hoped that the results of the study will be helpful in informing the understanding and decisions of librarians and others working to develop and promote IRs and green open access more broadly.

We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host's cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host. [ABSTRACT FROM AUTHOR]

The existence of sex chromosomes complicates the evolution of cosexuality (hermaphroditism). Four new genomic studies from haploid-dominant plants show commonalities and differences in mechanisms of the evolution of cosexuality, raising questions about the genetics of sexual dimorphism and the fate of cosexual lineages. [ABSTRACT FROM AUTHOR]

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged [...]

Intrachromosomal insertions are complex structural rearrangements that are challenging to interpret using classical cytogenetic methods. We report a male patient carrying a recombinant X chromosome derived from a maternally inherited intrachromosomal insertion. The patient exhibited developmental delay, intellectual disability, behavioral disorder, and dysmorphic facial features. To accurately identify the rearrangements in the abnormal X chromosome, additional cytogenetic studies were conducted, including fluorescence in situ hybridization (FISH), multicolor-banding FISH, and array comparative genomic hybridization. The results showed a recombinant X chromosome, resulting in a 13.05 Mb interstitial duplication of segment Xp22.33–Xp22.13, which was inserted at cytoband Xq26.1. The duplicated region encompasses 99 genes, some of which are associated with the patient's clinical manifestations. We propose that the combined effects of the Xp-duplicated genes may contribute to the patient's phenotype. [ABSTRACT FROM AUTHOR]