New Evidence of a Post-Laurentide Local Cirque Glacier on Mount Washington, New Hampshire

As global temperatures warmed and the last North American continental ice sheet receded there were several climate reversals during which time mean temperatures in New England were significantly reduced. Decreased temperatures in combination with increased precipitation may have supported the formation or reactivation of local mountain glaciers in pre-existing cirques on Mt. Washington, New Hampshire. Evidence supporting the existence of a local cirque glacier would provide important constraints on climatic conditions during the late-glacial Holocene transition. Preliminary mapping done in the area has identified a potential terminal moraine associated with a local valley glacier in the Great Gulf, the largest cirque-like feature on Mount Washington. The presence of this landform is significant because any pre-Wisconsin evidence of valley glaciers in the Great Gulf would likely have been expunged by the presence of continental ice. In order to determine the origins of the terminal moraine, representative samples of the till composing the moraine were collected by digging five test pits across the feature, sampling ~50 hand-sized stones from each pit, and determining the provenence of individual stones. Results indicate that the landform is composed of unsorted clasts with provenances of both local and regional origin. Clasts sourced within the Great Gulf support the interpretation that they were deposited by processes dependent on the presence of a local mountain glacier during a post-Wisconsin climate reversal. Stones of more distant origins may be attributed to residual till, associated with a continental ice mass that occupied the cirque at the time of local glacier reactivation. This data shows that the landform was deposited from processes taking place within the Great Gulf, and the pronounced topography and volume of the landform would support its interpretation as a terminal moraine. By reconstructing the glacier using the feature as terminus, a paleo-ELA was calculated and climate conditions necessary to promote the growth of an icemass were ascertained. Comparing this climate to the contemporary allows us to evaluate the magnitude of late-Pleistocene climate reversals in the White Mountains

Identification of a Small Regulatory RNA UspS Associated with the Universal Stress Protein in Lactobacillus Species

The gut microbiome is a complex habitat with many bacterial species, each playing crucial roles in regulating various physiological processes in the body. As the use of probiotics to combat human disease continues to increase, it is important to understand the mechanisms by which probiotic bacteria regulate their interactions with other bacteria and their host. Our exploration of the physiological functions of probiotic bacteria hopes to elucidate the role of small regulatory RNA (sRNA) in regulating gene expression within the microbiome. The goal of this project was to characterize the structure and function of the sRNA, UspS, which is found in probiotic, lactic acid bacteria. In Lactobacillus, UspS is closely associated with a downstream universal stress protein and contains an orphaned Lacto-usp RNA motif of unknown function. Computational methods have been used to study the UspS sRNA sequences from two Lactobacillus species in order to predict the secondary structures, generate 3D models, and search for potential mRNA interactions. Comparative sequence alignments and covariance analysis within the secondary structures predict a pseudoknot structure. The UspS sequence was isolated from two Lactobacillus species and sRNAs were synthesized by in vitro transcription with a T7 RNA polymerase. In preliminary studies, differential scanning fluorimetry of the UspS sRNA was able to confirm the presence of stable secondary structures. Future work will be focused on the structure of the pseudoknot region of UspS and its role in regulating the expression of the downstream universal stress protein

Comparative expression of Cbf genes in the Triticeae under different acclimation induction temperatures

In plants, the C-repeat binding factors (Cbfs) are believed to regulate low-temperature (LT) tolerance. However, most functional studies of Cbfs have focused on characterizing expression after an LT shock and have not quantified differences associated with variable temperature induction or the rate of response to LT treatment. In the Triticeae, rye (Secale cereale L.) is one of the most LT-tolerant species, and is an excellent model to study and compare Cbf LT induction and expression profiles. Here, we report the isolation of rye Cbf genes (ScCbfs) and compare their expression levels in spring- and winter-habit rye cultivars and their orthologs in two winter-habit wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) cultivars. Eleven ScCbfs were isolated spanning all four major phylogenetic groups. Nine of the ScCbfs mapped to 5RL and one to chromosome 2R. Cbf expression levels were variable, with stronger expression in winter- versus spring-habit rye cultivars but no clear relationship with cultivar differences in LT, down-stream cold-regulated gene expression and Cbf expression were detected. Some Cbfs were expressed only at warmer acclimation temperatures in all three species and their expression was repressed at the end of an 8-h dark period at warmer temperatures, which may reflect a temperature-dependent, light-regulated diurnal response. Our work indicates that Cbf expression is regulated by complex genotype by time by induction–temperature interactions, emphasizing that sample timing, induction–temperature and light-related factors must receive greater consideration in future studies involving functional characterization of LT-induced genes in cereals

Coagulase-Negative Staphylococcal Infections in the Neonatal Intensive Care Unit

Background. Coagulase-negative staphylococci (CoNS) are the most commonly isolated pathogens in the neonatal intensive care unit (NICU). CoNS infections are associated with increased morbidity, including neurodevelopmental impairment. Objective. To describe the epidemiology of CoNS infections in the NICU. To determine mortality among infants with definite, probable, or possible CoNS infections. Methods. We performed a retrospective cohort study of all blood, urine, and cerebrospinal fluid cultures from samples obtained from infants aged <121 postnatal days. Setting. A total of 248 NICUs managed by the Pediatrix Medical Group from 1997 to 2009. Results. We identified 16,629 infants with 17,624 episodes of CoNS infection: 1,734 (10%) definite, 3,093 (17%) probable, and 12,797 (73%) possible infections. Infants with a lower gestational age and birth weight had a higher incidence of CoNS infection. When controlling for gestational age, birth weight, and 5-minute Apgar score, we found that infants with definite, probable, or possible CoNS infection had lower mortality (odds ratio [OR], 0.74 [95% confidence interval {CI}: 0.61, 0.89], 0.68 [95% CI, 0.59, 0.79], and 0.69 [95% CI, 0.63, 0.76], respectively) compared with infants who had negative culture results ( P <.001). No significant difference in overall mortality was found in infants who had definite CoNS infection compared with those who had probable or possible CoNS infection (OR, 0.93 [95% CI, 0.75, 1.16] and 0.85 [95% CI, 0.70, 1.03], respectively). Conclusions. CoNS infection was strongly related to lower gestational age and birth weight. Infants with clinical sepsis and culture-positive CoNS infection had lower mortality rates than infants with clinical sepsis and negative blood culture results. No difference in mortality between infants with a diagnosis of definite, probable, or possible CoNS infection was observed

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript’s level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a ‘core’ module of antiviral genes is expressed very early by a few ‘precocious’ cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced ‘peaked’ inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.National Human Genome Research Institute (U.S.). Centers of Excellence in Genomic Science (1P50HG006193-01)National Institutes of Health (U.S.). Pioneer Award (DP1OD003958-01)Howard Hughes Medical InstituteBroad Institute of MIT and Harvard. Klarman Cell Observator

Single cell RNA Seq reveals dynamic paracrine control of cellular variation

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis, and function of gene expression variation between seemingly identical cells. Here, we sequence single-cell RNA-Seq libraries prepared from over 1,700 primary mouse bone marrow derived dendritic cells (DCs) spanning several experimental conditions. We find substantial variation between identically stimulated DCs, in both the fraction of cells detectably expressing a given mRNA and the transcript’s level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a “core” module of antiviral genes is expressed very early by a few “precocious” cells, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analyzing DCs from knockout mice, and modulating secretion and extracellular signaling, we show that this response is coordinated via interferon-mediated paracrine signaling. Surprisingly, preventing cell-to-cell communication also substantially reduces variability in the expression of an early-induced “peaked” inflammatory module, suggesting that paracrine signaling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations use to establish complex dynamic responses

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology