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The Hawaiian islands are recognized as a hotspot of biodiversity, including both surface and subsurface habitats. Recent studies of Hawaiian lava tube fauna have continued to reveal new species. Here, a new species of cave dwelling talitroid amphipod in the genus Spelaeorchestia is described from lava tubes on the island of Hawai i. It is compared with the only other known cave amphipod from the Hawaiian archipelago and with a closely related cave talitroid from Japan in the genus Minamitalitrus. 

Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization–Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

 

Here, we explicitly define a half-cell reaction approach for pH calculation using the electrode couple comprised of the solid-state chloride ion-selective electrode (Cl-ISE) as the reference electrode and the hydrogen ionselective ion-sensitive field effect transistor (ISFET) of the Honeywell Durafet as the hydrogen ion (H+)-sensitive measuring or working electrode. This new approach splits and isolates the independent responses of the Cl-ISE to the chloride ion (Cl−) (and salinity) and the ISFET to H+ (and pH), and calculates pH directly on the total scale (pHEXT total) in molinity (mol (kg-soln)−1) concentration units. We further apply and compare pHEXT total calculated using the half-cell and the existing complete cell reaction (defined by Martz et al. (2010)) approaches using measurements from two SeapHOx sensors deployed in a test tank. Salinity (on the Practical Salinity Scale) and pH oscillated between 1 and 31 and 6.9 and 8.1, respectively, over a six-day period. In contrast to established Sensor Best Practices, we employ a new calibration method where the calibration of raw pH sensor timeseries are split out as needed according to salinity. When doing this, pHEXT total had root-mean squared errors ranging between ±0.0026 and ±0.0168 pH calculated using both reaction approaches relative to pHtotal of the discrete bottle samples (pHdisc total). Our results further demonstrate the rapid response of the Cl-ISE reference to variable salinity with changes up to ±12 (30 min)−1. Final calculated pHEXT total were ≤±0.012 pH when compared to pHdisc total following salinity dilution or concentration. These results are notably in contrast to those of the few in situ field deployments over similar environmental conditions that demonstrated pHEXT total calculated using the Cl-ISE as the reference electrode had larger uncertainty in nearshore waters. Therefore, additional work beyond the correction of variable temperature and salinity conditions in pH calculation using the Cl-ISE is needed to examine the effects of other external stimuli on in situ electrode response. Furthermore, whereas past work has focused on in situ reference electrode response, greater scrutiny of the ISFET as the H+-sensitive measuring electrode for pH measurement in natural waters is also needed. 

Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due to the heterogeneity in environmental exposure and genetic background across subjects, subject effect contributes to the major source of variation in scRNA-seq data with multiple subjects, which severely confounds cell type specific differential expression (DE) analysis. Moreover, dropout events are prevalent in scRNA-seq data, leading to excessive number of zeroes in the data, which further aggravates the challenge in DE analysis.

We developed iDESC to detect cell type specific DE genes between two groups of subjects in scRNA-seq data. iDESC uses a zero-inflated negative binomial mixed model to consider both subject effect and dropouts. The prevalence of dropout events (dropout rate) was demonstrated to be dependent on gene expression level, which is modeled by pooling information across genes. Subject effect is modeled as a random effect in the log-mean of the negative binomial component. We evaluated and compared the performance of iDESC with eleven existing DE analysis methods. Using simulated data, we demonstrated that iDESC had well-controlled type I error and higher power compared to the existing methods. Applications of those methods with well-controlled type I error to three real scRNA-seq datasets from the same tissue and disease showed that the results of iDESC achieved the best consistency between datasets and the best disease relevance.

iDESC was able to achieve more accurate and robust DE analysis results by separating subject effect from disease effect with consideration of dropouts to identify DE genes, suggesting the importance of considering subject effect and dropouts in the DE analysis of scRNA-seq data with multiple subjects.

 

High altitude native populations exhibit physiological adaptations to environmental hypoxia. It has been hypothesized that two of these populations, Andeans and Tibetans, demonstrate distinct adaptive modes with the former characterized by increased blood oxygen content, and the latter characterized by increased blood flow. To investigate this hypothesis, we recruited two groups of healthy adults (ages 18-35) with highland ancestry who were born and currently reside at high altitude. The groups were: Andean Quechuas recruited in Cerro de Pasco, Peru (AND, n = 301) and Tibetan Sherpas recruited in Pheriche, Nepal (SHP, n = 64). Participants were tested in field laboratories using identical equipment and protocols, at nearly identical altitudes (4,330m and 4,371m, respectively). We assessed a wide variety of physiological variables at rest, submaximal exercise, and maximal exercise. We found that although some phenotypes aligned with the above hypothesis, the majority did not. For example, as predicted, AND displayed significantly lower (p<0.001) ventilatory equivalents for oxygen (VE/VO2) at rest. However, this trend reversed at maximal exercise, with AND displaying significantly higher (p<0.001) VE/VO2 than SHP. Further, contrary to the above hypothesis, we found no statistically significant differences in flow-mediated dilation between the groups. These results suggest that the adaptive modes of these populations are perhaps not as distinct as previously supposed. Given that this hypothesis was formulated on the basis of data taken at rest, our data highlights the importance of assessing physiology both at rest and exercise, to gain a more complete understanding of adaptation to high altitude. 

Accurate reconstruction of Laurentide Ice Sheet volume changes following the Last Glacial Maximum is critical for understanding ice sheet contribution to sea-level rise, the resulting influence of meltwater on oceanic circulation, and the spatial and temporal patterns of deglaciation. Here, we provide empirical constraints on Laurentide Ice Sheet thinning during the last deglaciation by measuring in situ cosmogenic 10Be in 81 samples collected along vertical transects of nine mountains in the northeastern United States. In conjunction with 107 exposure age samples over five vertical transects from previous studies, we reconstruct ice sheet thinning history. At peripheral sites (within 200 km of the terminal moraine), we find evidence for ∼600 m of thinning between 19.5 ka and 17.5 ka, which is coincident with the slow initial margin retreat indicated by varve records. At locations >400 km north of the terminal moraine, exposure ages above and below 1200 m a.s.l. exhibit different patterns. Ages above this elevation are variable and older, while lower elevation ages are indistinguishable over 800−1000 m elevation ranges, a pattern that suggests a subglacial thermal boundary at ∼1200 m a.s.l. separating erosive, warm-based ice below and polythermal, minimally erosive ice above. Low-elevation ages from up-ice mountains are between 15 ka and 13 ka, which suggests rapid thinning of ∼1000 m coincident with Bølling-Allerød warming. These rates of rapid paleo-ice thinning are comparable to those of other vertical exposure age transects around the world and may have been faster than modern basin-wide thinning rates in Antarctica and Greenland, which suggests that the southeastern Laurentide Ice Sheet was highly sensitive to a warming climate. 

Engineered whole lungs may one day expand therapeutic options for patients with end-stage lung disease. However, the feasibility of ex vivo lung regeneration remains limited by the inability to recapitulate mature, functional alveolar epithelium. Here, we modulate multimodal components of the alveolar epithelial type 2 cell (AEC2) niche in decellularized lung scaffolds in order to guide AEC2 behavior for epithelial regeneration. First, endothelial cells coordinate with fibroblasts, in the presence of soluble growth and maturation factors, to promote alveolar scaffold population with surfactant-secreting AEC2s. Subsequent withdrawal of Wnt and FGF agonism synergizes with tidal-magnitude mechanical strain to induce the differentiation of AEC2s to squamous type 1 AECs (AEC1s) in cultured alveoli, in situ. These results outline a rational strategy to engineer an epithelium of AEC2s and AEC1s contained within epithelial-mesenchymal-endothelial alveolar-like units, and highlight the critical interplay amongst cellular, biochemical, and mechanical niche cues within the reconstituting alveolus.