Colby College

A recent study published in Oryx proposed that the extinct Javan tiger Panthera tigris sondaica may still survive on the Island of Java, Indonesia, based on mitochondrial DNA analysis of a single hair sample collected from a location where a tiger was reportedly encountered. However, upon reanalysing the genetic data presented in that study, we conclude that there is little support for this claim. The sequences of the putative tiger hair and Javan tiger museum specimens generated are not from tiger cytoplasmic mitochondrial DNA but more likely the nuclear pseudogene copies of mitochondrial DNA. In addition, the number of mismatches between the two Javan tiger sequences is unusually high for homologous sequences that are both from tigers, suggesting potential issues with data reliability. The paper provides insufficient details on quality control measures, making it impossible to rule out the possibility that errors were introduced during the analysis. Consequently, it is inappropriate to use the sequences presented in that study to infer the existence of the Javan tiger.

We use thin position of Heegaard splittings to give a new proof of Haken’s Lemma that a Heegaard surface of a reducible manifold is reducible and of Scharlemann’s “Strong Haken Theorem”: a Heegaard surface for a 3-manifold may be isotoped to intersect a given collection of essential spheres and discs in a single loop each. We also give a reformulation of Casson and Gordon’s theorem on weakly reducible Heegaard splittings, showing that they exhibit additional structure with respect to certain incompressible surfaces. This article could also serve as an introduction to the theory of generalized Heegaard surfaces and it includes a careful study of their behavior under amalgamation.

Mental health concerns are prevalent among college students, highlighting the need for effective interventions that promote self-awareness and holistic well-being. MindScape explores a novel approach to AI-powered journaling by integrating passively collected behavioral patterns such as conversational engagement, sleep, and location with Large Language Models (LLMs). This integration creates a highly personalized and context-aware journaling experience, enhancing self-awareness and well-being by embedding behavioral intelligence into AI. We present an 8-week exploratory study with 20 college students, demonstrating the MindScape app's efficacy in enhancing positive affect (7%), reducing negative affect (11%), loneliness (6%), and anxiety and depression, with a significant week-over-week decrease in PHQ-4 scores (-0.25 coefficient). The study highlights the advantages of contextual AI journaling, with participants particularly appreciating the tailored prompts and insights provided by the MindScape app. Our analysis also includes a comparison of responses to AI-driven contextual versus generic prompts, participant feedback insights, and proposed strategies for leveraging contextual AI journaling to improve well-being on college campuses. By showcasing the potential of contextual AI journaling to support mental health, we provide a foundation for further investigation into the effects of contextual AI journaling on mental health and well-being.

The rearrangement of 2-norbornylidene carbene into the strained bicyclo[3.2.1]oct-2-yne preferentially involves migration of a tertiary carbon over a secondary carbon, as determined by 13C labelling experiments. This trend contrasts with...

Preterm birth (PTB; <37 weeks completed gestation) is a devastating problem affecting over 13 million live births worldwide. In the U.S., African Americans experience significantly higher rates of PTB compared to non-Hispanic Whites. PTB disparities have been linked to social determinants of health (e.g., socioeconomic status, discrimination). However, the biological underpinnings related to these associations are unclear. DNA methylation (DNAm) is subject to environmental influences, and DNAm modifications are known to affect gene expression. Using a multi-omic approach, we examined differences in combined DNA methylation (DNAm) and messenger RNA (mRNA) transcriptomic data from 20 pregnant African American women (12 PTB; 8 term birth) early in pregnancy (8–18 weeks gestation). We found that the HLA- DQB2 gene was both differentially methylated (cg12296550; p = .02) and differentially expressed ( p = .014; log2FC = 2.5) between women with PTB and term birth. Gene expression analysis showed HLA- DQB2 and HLA- DRB4 ( p = .028; log2FC = −3.6) were the two most highly expressed genes. HLA-DQB2 expressed higher in PTB and HLA- DRB4 expressed higher in term birth. However, no genes remained significant ( p < .05) after Bonferroni correction. HLA- DRB4 and AKR1C1 were identified as a potential biomarkers in dimensionality reduction models and are also important to immune function and allogenic breakdown. Altered gene expression may lead to inflammatory imbalances or allogenic intolerance resulting in PTB. This study provides proof-of-concept evidence for the feasibility and importance of future multi-omics studies with larger populations to further explore the genes and pathways identified here.

For many decades, ecologists have sought to understand the extent to which species losses lead to secondary extinctions—that is, the additional loss of species that occurs when resources or key interactions are lost (i.e. robustness). In particular, ecologists aim to identify generalisable rules that explain which types of food webs are more or less robust to secondary extinctions. Food web structure, or the patterns formed by species and their interactions, has been extensively studied as a potential factor that influences robustness to species loss. We systematically reviewed 28 studies to identify the relationships between food web structure and robustness to species loss and how the conclusions depend on methodological differences. Contrary to popular belief and theory, we found relatively consistent, positive relationships between connectance and robustness, among other generalities. Yet, we also found that conflicting conclusions about structure‐robustness relationships can be, in part, attributed to differences in the type of data that studies use, particularly studies that use empirical data versus those generated from theoretical models. This review points towards a need to standardise methodology to answer the open question of whether robustness and its relationship with food web structure and to provide applicable insights for managing complex systems.

We examine the identity tensions of an online volunteer English teacher at a rural village school in southwestern China to uncover the structural inequalities embedded in her everyday teaching and identity work. Adopting narrative ethnographic methods, we conducted thematic analysis of data from interviews and classroom observations. Findings show that Jing's identity tensions derived from the challenges of transitioning to a new school context and a different mode of instruction, as well as navigating the conflicts between personal values, institutional demands, and structural constraints. The study suggests that online volunteer teachers attempting to address the needs of rural underserved students may experience multifaceted dimensions of identity tensions due to the lack of understanding of local pedagogies, and student backgrounds, as well as the social and policy constraints beyond classrooms.

A multitude of JWST studies reveal a surprising over-abundance of over-massive accreting super-massive black holes (SMBHs) -- leading to a deepening tension between theory and observation in the first billion years of cosmic time. Across X-ray to infrared wavelengths, models built off of pre-JWST predictions fail to easily reproduce observed AGN signatures (or lack thereof), driving uncertainty around the true nature of these sources. Using a sample of JWST AGN identified via their broadened Halpha emission and covered by the deepest X-ray surveys, we find neither any measurable X-ray emission nor any detection of high-ionization emission lines frequently associated with accreting SMBHs. We propose that these sources are accreting at or beyond the Eddington limit, which reduces the need for efficient production of heavy SMBH seeds at cosmic dawn. Using a theoretical model of super-Eddington accretion, we can produce the observed relative dearth of both X-ray and ultraviolet emission, as well as the high Balmer decrements, without the need for significant dust attenuation. This work indicates that super-Eddington accretion is easily achieved through-out the early Universe, and further study is required to determine what environments are required to trigger this mode of black hole growth.

The superficial white matter (SWM) consists of numerous short‐range association fibers connecting adjacent and nearby gyri and plays an important role in brain function, development, aging, and various neurological disorders. Diffusion MRI (dMRI) tractography is an advanced imaging technique that enables in vivo mapping of the SWM. However, detailed imaging of the small, highly‐curved fibers of the SWM is a challenge for current clinical and research dMRI acquisitions. This work investigates the efficacy of mapping the SWM using in vivo ultra‐high‐resolution dMRI data. We compare the SWM mapping performance from two dMRI acquisitions: a high‐resolution 0.76‐mm isotropic acquisition using the generalized slice‐dithered enhanced resolution (gSlider) protocol and a lower resolution 1.25‐mm isotropic acquisition obtained from the Human Connectome Project Young Adult (HCP‐YA) database. Our results demonstrate significant differences in the cortico‐cortical anatomical connectivity that is depicted by these two acquisitions. We perform a detailed assessment of the anatomical plausibility of these results with respect to the nonhuman primate (macaque) tract‐tracing literature. We find that the high‐resolution gSlider dataset is more successful at depicting a large number of true positive anatomical connections in the SWM. An additional cortical coverage analysis demonstrates significantly higher cortical coverage in the gSlider dataset for SWM streamlines under 40 mm in length. Overall, we conclude that the spatial resolution of the dMRI data is one important factor that can significantly affect the mapping of SWM. Considering the relatively long acquisition time, the application of dMRI tractography for SWM mapping in future work should consider the balance of data acquisition efforts and the efficacy of SWM depiction.

Strained cycloalkynes are valuable building blocks in synthetic chemistry due to their high degree of reactivity and ability to form structurally complex scaffolds, common features of many pharmaceuticals and natural products. Alkylidene carbenes provide a pathway to the formation of strained cycloalkynes through Fritsch–Buttenberg–Wiechell rearrangements, but this strategy, like other methods of alkyne generation, is believed to depend upon a thermodynamic equilibrium that favors the alkyne over the carbene. Herein three highly strained, polycyclic alkynes, previously thought to be thermodynamically inaccessible, are generated under mild conditions and intercepted through Diels–Alder cycloaddition with a diene trapping agent. The use of a different trapping agent also allows for the interception of the alkylidene carbene, providing the first instance in which both an exocyclic alkylidene carbene and its cycloalkyne Fritsch–Buttenberg–Wiechell rearrangement product have been trapped.

An industrial-era decline in Greenland ice-core methanesulfonic acid is thought to herald a collapse in North Atlantic marine phytoplankton stocks related to a weakening of the Atlantic meridional overturning circulation. By contrast, stable levels of total marine biogenic sulfur contradict this interpretation and point to changes in atmospheric oxidation as a potential cause of the methanesulfonic acid decline. However, the impact of oxidation on methanesulfonic acid production has not been quantified, nor has this hypothesis been rigorously tested. Here we present a multi-century methanesulfonic acid record from the Denali, Alaska, ice core, which shows a methanesulfonic acid decline similar in magnitude but delayed by 93 years relative to the Greenland record. Box-model results using updated dimethyl sulfide oxidation pathways indicate that oxidation by pollution-driven nitrate radicals has suppressed atmospheric methanesulfonic acid production, explaining most, if not all, of Denali’s and Greenland’s methanesulfonic acid declines without requiring a change in phytoplankton production. The delayed timing of the North Pacific methanesulfonic acid decline, relative to the North Atlantic, reflects the distinct history of industrialization in upwind regions and is consistent with the Denali and Greenland ice-core nitrate records. These results demonstrate that multidecadal trends in industrial-era Arctic ice-core methanesulfonic acid reflect rising anthropogenic pollution rather than declining marine primary production.

Sumoylation, a process in which SUMO (small ubiquitin like modifier) is conjugated to target proteins, emerges as a post-translational modification that mediates protein−protein interactions, protein complex assembly, and localization of target proteins. The coordinated actions of SUMO ligases, proteases, and SUMO-targeted ubiquitin ligases determine the net result of sumoylation. It is well established that sumoylation can somewhat promiscuously target proteins in groups as well as selectively target individual proteins. Through changing protein dynamics, sumoylation orchestrates multi-step processes in chromatin biology. Sumoylation influences various steps of mitosis, DNA replication, DNA damage repair, and pathways protecting chromosome integrity. This review highlights examples of SUMO-regulated nuclear processes to provide mechanistic views of sumoylation in DNA metabolism.