Production of Heterocyst Glycolipids and Glycerol Dialkyl Glycerol Tetraether membrane lipids in the water column of a stratified tropical lake, Malawi, Africa

Temperature is a critical component of paleoenvironmental reconstructions, yet it is notoriously difficult to measure in terrestrial archives. Presented here is an investigation of the sources and distributions of archaeal and bacterial glycerol dialkyl glycerol tetraethers (GDGTs) and cyanobacterial heterocyst glycolipids (HGs) in Lake Malawi. The study aims to evaluate the potential for these lipids to function as paleotemperature proxies in tropical lacustrine environments. GDGTs and HGs were extracted from settling particulate matter (SPM) collected at bi-monthly intervals from 2011 – 2013. Sediment traps used to collect SPM were moored in both the north and south basins of Lake Malawi in order to evaluate spatial trends, in addition to temporal trends, in lipid production and export across the lake. Distributions of isoprenoid GDGTs indicate that Thaumarchaeota are the dominant GDGT-producing archaea in the surface waters of Lake Malawi. However, TEX86-based temperatures do not track lake surface temperatures at either the northern or southern sediment trap locations. TEX86 in the north basin instead reflects surface water temperatures at the time of maximum Thaumarchaeota activity, while TEX86 in the south basin records patterns in seasonal upwelling that possibly drive shifts in the membrane composition of Thaumarchaeota or in the dominant planktonic archaeal community. Branched GDGTs are likely produced by distinct groups of bacteria within the water column, complicating the interpretation of temperatures reconstructed from their distributions. The inability of available branched GDGT calibrations to produce reasonable temperatures underscores the need for comprehensive studies of autochthonous branched GDGT production in lakes. Bulk sedimentation is the primary driver of branched and isoprenoid GDGT export in the metalimnion. HGs are present throughout the time-series, but maximum fluxes occur in December. HGs in SPM are sourced from actively living cyanobacteria populations, indicating rapid export of the lipids through the water column. Temperatures reconstructed with published HG-based indices do not match the seasonal variability in surface temperatures, however the fractional abundances of HG diols with C26 and C28 side chains do appear related to lake temperatures in this system. The production of C28 HG keto-ols may also be associated with heterocyst differentiation

Deep drilling at the Chalco lake:A technical report

En este artículo se presenta un resumen de las actividades realizadas para la recuperación de la totalidad de la secuencia lacustre del lago de Chalco. Mediante estudios geofísicos se determinó la distribución y espesor de los sedimentos lacustres con base en lo cual se seleccionó el sitio de perforación. Con datos de los espectros H/V de sísmica pasiva se hizo un mapa de isofrecuencias que definieron una región con sedimentos lacustres y material volcánico granulado de hasta 300 m de espesor. El uso de métodos electromagnéticos mostró cambios en la resistividad eléctrica relacionados con variaciones en la composición de la columna sedimentaria; entre 100 – 120 m de profundidad hay un primer aumento en la resistividad asociado al incremento de materiales volcaniclásticos, y entre 330 – 400 m de profundidad un segundo aumento asociado a la presencia de coladas de basalto. Fueron perforados tres pozos con recuperación continua, llegando a profundidades de 420 m en el pozo A, 310 m en el B y 520 en el C. Durante el trabajo de perforación se tomaron muestras para el análisis geomicrobiológicos y de metagenómica. Durante el proceso de perforación se recuperó un total de 1152 m de sedimentos con una profundidad máxima de 520 m. El porcentaje de recuperación de la columna sedimentaria varió entre 88 a 92 % en los tres sondeos. Los resultados del análisis de susceptibilidad magnética en las tres secuencias indica que los primeros 260 m son sedimentos lacustres, entre 260 y 300 m los sedimentos son más gruesos y debajo de los 300 m son predominantemente volcaniclásticos. El análisis de la secuencia sedimentaria del lago de Chalco de los últimos ~300000 años, permitirá documentar y ampliar el conocimiento acerca de la variabilidad climática de la zona, la historia paleoambiental, la historia del cierre de la cuenca, el desarrollo del sistema lacustre y la recurrencia de la actividad volcánica en la cuenca. Además, el estudio de las propiedades físicas de esta secuencia sedimentaria es importante para la modelación de la propagación de ondas sísmicas y de la estructura de la cuenca, así como para mejorar la capacidad de modelación del proceso de subsidencia del terreno que experimenta esta región. This paper presents a short description of the coring operations undertaken to recover the full lacustrine sedimentary sequence from Chalco. Geophysical techniques were used to determine the distribution and thickness of the sediments in order to select the drilling site. Resonance frequencies determined from H/V spectral ratios were used to determine an area where lake sediments reached 300 m thickness. Electromagnetic survey showed two changes in electric resistivity which were related to changes in sediment composition, the first from 100 to 120 m, related to an increase in volcanoclastic sediments and the second from 330 to 400 m related to the presence of a basaltic flows. Three wells were drilled with continuous recovery, reaching depths of 420 m in well A, 310 in B and 520 in C. Samples for geomicrobiological and metagenomics studies were collected during drilling operations. A total of 1152 m of core sediments were recovered reaching a maximum depth of 520 m. Recovery percentages were between 88 and 92 % in the three wells. Magnetic susceptibility analyses in the three sequences show that the first 260 m are mostly lake sediments, between 260 and 300 m sediments are coarser and below 300 m they are mostly volcaniclastic. Analysis of the sedimentary sequence of Lake Chalco that covers the last ~300000 years will allow documenting and extending the knowledge of climate variability in area, the paleoenvironmental history, basin closure history, lacustrian system development and volcanic activity recurrence. Studies of the physical properties of this sequence will be important for seismic propagation and basin structure modeling, and also will improve modeling of the subsidence process that this region experiences

Glacial-Interglacial Variability of Eastern Pacific Hydroclimate

Unprecedented drought conditions in southwest North America (SWNA, defined as the region from southern California to southern Mexico, west of the continental divide) has raised alarms regarding water resource scarcity in a region with dense urban populations and vital agricultural industries. Modern hydroclimate in SWNA is complex as rainfall seasonality and moisture source ranges from the Mediterranean climate of California, bimodal desert southwest, monsoonal northwest Mexico, and Central American tropics, and there is a high degree of interannual rainfall variability due to the importance of short-lived, high-intensity events to regional moisture budgets. A deeper understanding of the spatio-temporal patterns of mean annual and seasonal rainfall variability and their response to global climate perturbations is thus critical for future planning and water resource management in the region. The eastern Pacific is a key modulator of rainfall variability in SWNA. Pacific ocean-atmosphere interactions affect North American monsoon intensity, the seasonal migration of the intertropical convergence zone (ITCZ), the strength, location, and waviness of the mid-latitude storm tracks, and the occurrence of extreme precipitation events associated with atmospheric rivers, tropical cyclones, and the El Niño/Southern Oscillation. Paleoclimate records from the Pacific can provide crucial constraints on how these processes responded to past global climate perturbations. A unified view of Pacific-North American interactions is currently limited by sparse proxy data from the Eastern Pacific Warm Pool (EPWP) and the Gulf of California, specifically of reconstructions that extend beyond the Last Glacial Maximum (LGM; 19--23 ka). The work presented in this dissertation sheds new light onto the late Pleistocene climatic history of SWNA based on novel organic geochemical proxy reconstructions of eastern Pacific sea surface temperatures and North American monsoon rainfall variability. The proxy data indicate that the northern EPWP (along the northwest Mexican Margin near the mouth of the Gulf of California) did not experience glacial cooling. Rather, elevated sea surface temperatures regularly occur during intervals of low greenhouse gases and increased global ice volume across the last glacial cycle. Meanwhile, monsoonal rainfall was elevated during warm interglacials and suppressed during glacial periods. I additionally compare the proxy data to general circulation model simulations of the LGM and Last Interglacial (LIG; $\sim$117--130 ka) periods to investigate the effects of orbital forcing (insolation), greenhouse gases, and ice sheets on moisture source, precipitation seasonality and geographic patterns of rainfall variability across SWNA. This research fills a critical data gap and ultimately provides a mechanistic understanding of the patterns and drivers of hydroclimate variability in SWNA that indicates a complexity in the response of SWNA temperature and precipitation to global climate forcings

Sharing Science thru Storytelling (2018 Ocean Sciences)

Slides from a science communication workshop presented at 2018 Ocean Sciences meeting in Portland Oregon (12 Feb 2018). <br>(Version 1, 2 are the same, just updated author and categories)<br

The vertical distribution of Thaumarchaeota in the water column of Lake Malawi inferred from core and intact polar tetraether lipids

Several long paleoclimate records generated from Lake Malawi sediments rely on an assumption that the TEX86 paleothermometer reflects annual mean lake surface temperatures. Thaumarchaeota, the producers of the isoprenoid glycerol dialkyl glycerol tetraether (iGDGT) lipids that are the basis of the TEX86 proxy, can occupy a wide range of habitats in the upper water column of lacustrine systems, so it is crucial to specifically constrain the ecology of Thaumarchaeota in Lake Malawi to properly interpret its sedimentary TEX86 record. To investigate the spatial and vertical distribution of Thaumarchaeotal iGDGT production in Lake Malawi, suspended particulate matter (SPM) was collected from the upper water column (>300 m) at three sites spanning the north, central, and south basins of the lake and analyzed for intact polar (IPL) and core (CL) iGDGT lipid abundances. Samples were collected in January during the austral summer when the lake is strongly stratified. Concentrations of the most labile IPL, hexose-phosphohexose (HPH)-crenarchaeol, were greatest just below the deep chlorophyll maximum at ∼50 m water depth in the deeper north and central basins and ∼30 m in the shallow south basin. Maximum CL concentrations occur below the maximum HPH-crenarchaeol concentrations and therefore possibly reflect the accumulation of recently produced IPL GDGT degradation products. If the export of CLs to the sediments is dominated by this CL pool, sedimentary TEX86 would reflect Thaumarchaeota living within the thermocline during the stratified season and therefore may have a cool bias rather than reflecting true surface water temperatures. An increase in abundances of GDGT-2, crenarchaeol isomer, and monohexose (MH)-crenarchaeol at ∼150–200 m suggests that a secondary Thaumarchaeotal population, likely Group I.1b Thaumarchaeota, inhabits the subsurface water column near the anoxic-suboxic boundary. Total production of iGDGTs by this group appears to be much lower than the surface-dwelling clade, but its imprint on sedimentary TEX86 is unknown. An analysis of iGDGT production in the water column throughout the annual cycle is needed to resolve the timing and magnitude of export of CLs to the sediments from these two Thaumarchaeotal populations

The vertical distribution of Thaumarchaeota in the water column of Lake Malawi inferred from core and intact polar tetraether lipids

Several long paleoclimate records generated from Lake Malawi sediments rely on an assumption that the TEX86 paleothermometer reflects annual mean lake surface temperatures. Thaumarchaeota, the producers of the isoprenoid glycerol dialkyl glycerol tetraether (iGDGT) lipids that are the basis of the TEX86 proxy, can occupy a wide range of habitats in the upper water column of lacustrine systems, so it is crucial to specifically constrain the ecology of Thaumarchaeota in Lake Malawi to properly interpret its sedimentary TEX86 record. To investigate the spatial and vertical distribution of Thaumarchaeotal iGDGT production in Lake Malawi, suspended particulate matter (SPM) was collected from the upper water column (>300 m) at three sites spanning the north, central, and south basins of the lake and analyzed for intact polar (IPL) and core (CL) iGDGT lipid abundances. Samples were collected in January during the austral summer when the lake is strongly stratified. Concentrations of the most labile IPL, hexose-phosphohexose (HPH)-crenarchaeol, were greatest just below the deep chlorophyll maximum at ∼50 m water depth in the deeper north and central basins and ∼30 m in the shallow south basin. Maximum CL concentrations occur below the maximum HPH-crenarchaeol concentrations and therefore possibly reflect the accumulation of recently produced IPL GDGT degradation products. If the export of CLs to the sediments is dominated by this CL pool, sedimentary TEX86 would reflect Thaumarchaeota living within the thermocline during the stratified season and therefore may have a cool bias rather than reflecting true surface water temperatures. An increase in abundances of GDGT-2, crenarchaeol isomer, and monohexose (MH)-crenarchaeol at ∼150–200 m suggests that a secondary Thaumarchaeotal population, likely Group I.1b Thaumarchaeota, inhabits the subsurface water column near the anoxic-suboxic boundary. Total production of iGDGTs by this group appears to be much lower than the surface-dwelling clade, but its imprint on sedimentary TEX86 is unknown. An analysis of iGDGT production in the water column throughout the annual cycle is needed to resolve the timing and magnitude of export of CLs to the sediments from these two Thaumarchaeotal populations

Detailed outline of the tasks undertaken during AcWriMo at Maynooth University Library

<div><p>Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause (40–50%) of chronic kidney disease (CKD) in children. About 40 monogenic causes of CAKUT have so far been discovered. To date less than 20% of CAKUT cases can be explained by mutations in these 40 genes. To identify additional monogenic causes of CAKUT, we performed whole exome sequencing (WES) and homozygosity mapping (HM) in a patient with CAKUT from Indian origin and consanguineous descent. We identified a homozygous missense mutation (c.1336C>T, p.Arg446Cys) in the gene <i>Von Willebrand factor A domain containing 2</i> (<i>VWA2</i>). With immunohistochemistry studies on kidneys of newborn (P1) mice, we show that Vwa2 and Fraser extracellular matrix complex subunit 1 (Fras1) co-localize in the nephrogenic zone of the renal cortex. We identified a pronounced expression of Vwa2 in the basement membrane of the ureteric bud (UB) and derivatives of the metanephric mesenchyme (MM). By applying <i>in vitro</i> assays, we demonstrate that the Arg446Cys mutation decreases translocation of monomeric VWA2 protein and increases translocation of aggregated VWA2 protein into the extracellular space. This is potentially due to the additional, unpaired cysteine residue in the mutated protein that is used for intermolecular disulfide bond formation. VWA2 is a known, direct interactor of FRAS1 of the Fraser-Complex (FC). FC-encoding genes and interacting proteins have previously been implicated in the pathogenesis of syndromic and/or isolated CAKUT phenotypes in humans. <i>VWA2</i> therefore constitutes a very strong candidate in the search for novel CAKUT-causing genes. Our results from <i>in vitro</i> experiments indicate a dose-dependent neomorphic effect of the Arg446Cys homozygous mutation in <i>VWA2</i>.</p></div

Reduced secretion and intracellular and extracellular aggregation of Arg446Cys VWA2.

<p><b>(a)</b> Cell culture supernatants and cell lysates from wild type (wt) and Arg446Cys VWA2 (R446C) expressing 293EBNA cells were separated by SDS-PAGE under reducing and non-reducing conditions and detected with an antibody against the One-STrEP-tag. Arrowheads indicate monomeric VWA2. On the right, equal loading is demonstrated by Ponceau staining of the membranes. Asterisks indicate artefact bands. <b>(b)</b> cDNA from non transfected (nt), non-transfected ER stress induced (nt+DTT), wt VWA2 transfected (wt) and Arg446Cys VWA2 (R446C) transfected 293EBNA cells was submitted to RT-PCR and the PCR products separated by agarose gel electrophoresis. Arrows indicate the bands for XBP-1 and ER stress induced XBP-1s. Equal loading is demonstrated by actin control RT-PCR shown below. <b>(c)</b> Equal amounts (0.2 μg) of affinity purified wild type (wt) and Arg446Cys VWA2 (R446C) were separated by SDS-PAGE under reducing and non-reducing conditions and detected with an antibody against the C-terminal fragment (P3) of human VWA2. Under non-reducing conditions higher aggregates are seen. Arrows indicate the border between separation and stacking gel. (d) Equal amounts of cell culture supernatants and cell lysates from wild type (wt) and Arg446Cys VWA2 (R446C) expressing 293EBNA cells as in (a) and of affinity purified wild type (wt) and Arg446Cys VWA2 (R446C) as in (b) were separated by agarose-polyacrylamide composite gels under non-reducing conditions and detected with an antibody against the One-STrEP-tag.</p