Distribution, morphology, and genetic affinities of dwarf embedded Fucus populations from the Northwest Atlantic Ocean

Dwarf embedded Fucus populations in the Northwest Atlantic Ocean are restricted to the upper intertidal zone in sandy salt marsh environments; they lack holdfasts and are from attached parental populations of F. spiralis or F. spiralis x F. vesiculosus hybrids after breakage and entanglement with halophytic marsh grasses. Dwarf forms are dichotomously branched, flat, and have a mean overall length and width of 20.3 and 1.3 mm, respectively. Thus, they are longer than Irish (mean 9.3 mm) and Alaskan (mean 15.0 mm) populations identified as F cottonii. Reciprocal transplants of different Fucus taxa in a Maine salt marsh confirm that F spiralis can become transformed into dwarf embedded thalli within the high intertidal zone, while the latter can grow into F. s. ecad lutarius within the mid intertidal zone. Thus, vertical transplantation can modify fucoid morphology and result in varying ecads. Microsatellite markers indicate that attached F spiralis and F vesiculosus are genetically distinct, while dwarf forms may arise via hybridization between the two taxa. The ratio of intermediate to species-specific-genotypes decreased with larger thalli. Also, F s. ecad lutarius consists of a mixture of intermediate and pure genotypes, while dwarf thalli show a greater frequency of hybrids

Human-induced changes in the distribution of rainfall

A likely consequence of global warming will be the redistribution of Earth’s rain belts, affecting water availability for many of Earth’s inhabitants. We consider three ways in which planetary warming might influence the global distribution of precipitation. The first possibility is that rainfall in the tropics will increase and that the subtropics and mid-latitudes will become more arid. A second possibility is that Earth’s thermal equator, around which the planet’s rain belts and dry zones are organized, will migrate northward. This northward shift will be a consequence of the Northern Hemisphere, with its large continental area, warming faster than the Southern Hemisphere, with its large oceanic area. A third possibility is that both of these scenarios will play out simultaneously. We review paleoclimate evidence suggesting that (i) the middle latitudes were wetter during the last glacial maximum, (ii) a northward shift of the thermal equator attended the abrupt Bølling-Allerød climatic transition ~14.6 thousand years ago, and (iii) a southward shift occurred during the more recent Little Ice Age. We also inspect trends in seasonal surface heating between the hemispheres over the past several decades. From these clues, we predict that there will be a seasonally dependent response in rainfall patterns to global warming. During boreal summer, in which the rate of recent warming has been relatively uniform between the hemispheres, wet areas will get wetter and dry regions will become drier. During boreal winter, rain belts and drylands will expand northward in response to differential heating between the hemispheres

Hydrologic Impacts of Past Shifts of Earth’s Thermal Equator Offer Insight into Those to be Produced by Fossil Fuel CO2

Major changes in global rainfall patterns accompanied a northward shift of Earth’s thermal equator at the onset of an abrupt climate change 14.6 kya. This northward pull of Earth’s wind and rain belts stemmed from disintegration of North Atlantic winter sea ice cover, which steepened the interhemispheric meridional temperature gradient. A southward migration of Earth’s thermal equator may have accompanied the more recent Medieval Warm to Little Ice Age climate transition in the Northern Hemisphere. As fossil fuel CO2 warms the planet, the continents of the Northern Hemisphere are expected to warm faster than the Southern Hemisphere oceans. Therefore, we predict that a northward shift of Earth’s thermal equator, initiated by an increased interhemispheric temperature contrast, may well produce hydrologic changes similar to those that occurred during past Northern Hemisphere warm periods. If so, the American West, the Middle East, and southern Amazonia will become drier, and monsoonal Asia, Venezuela, and equatorial Africa will become wetter. Additional paleoclimate data should be acquired and model simulations should be conducted to evaluate the reliability of this analog

How did the hydrologic cycle respond to the two-phase mystery interval?

Lake Estancia’s transition from a Big Dry episode during the first half of the Mystery Interval to a Big Wet episode during the second half has equivalents in records from across the planet. At the time of this transition, Chinese monsoons experienced pronounced weakening, closed-basin lakes in both the Great Basin of the western United States and in the southern Altiplano of South America underwent a major expansion, mountain glaciers in Southern Hemisphere middle latitudes had retreated, and the rates of increase of CO2 and of d18O in Antarctic ice underwent a decrease. Finally, the precipitous drop in dust rain over Antarctica and the Southern Ocean terminated as did a similar drop in the 13C to 12C ratio in atmospheric CO2. These changes are consistent with a southward shift of the thermal equator. The cause of such a shift is thought to be an expansion of sea ice caused by a shutdown in deep water production in the northern Atlantic. This creates a dilemma because a similar southward shift is an expected consequence of the Heinrich event #1 which initiated the Mystery Interval

A Study of the Direct-Fitting Method for Measurement of Galaxy Velocity Dispersions

We have measured the central stellar velocity dispersions of 33 nearby spiral and elliptical galaxies, using a straightforward template-fitting algorithm operating in the pixel domain. The spectra, obtained with the Double Spectrograph at Palomar Observatory, cover both the Ca triplet and the Mg b region, and we present a comparison of the velocity dispersion measurements from these two spectral regions. Model fits to the Ca triplet region generally yield good results with little sensitivity to the choice of template star. In contrast, the Mg b region is more sensitive to template mismatch and to details of the fitting procedure such as the order of a polynomial used to match the continuum shape of the template to the object. As a consequence of the correlation of the [Mg/Fe] ratio with velocity dispersion, it is difficult to obtain a satisfactory model fit to the Mg b lines and the surrounding Fe blends simultaneously, particularly for giant elliptical galaxies with large velocity dispersions. We demonstrate that if the metallicities of the galaxy and template star are not well matched, then direct template-fitting results are improved if the Mg b lines themselves are excluded from the fit and the velocity dispersion is determined from the surrounding weaker lines.Comment: 14 pages. To appear in A

Rational modification of an HIV-1 gp120 results in enhanced neutralization breadth when used as a DNA prime

Background The identification of phenotypic features of the HIV-1 envelope glycoprotein that correlate with neutralization breadth is an important goal of HIV vaccine research. Recently we compared the immunogenic potential of two gp120s differing in their ability to utilize CD4; B33 (highly macrophage topic) and LN40 (non-macrophage tropic). Using a DNA prime protein boost regimen in New Zealand White Rabbits, LN40-primed sera displayed enhanced breadth compared to the B33-primed group, with differences in immunogenicity between groups modulated by specific residues within and flanking the V3 loop and the CD4bs. To better understand the role of these residues in eliciting breadth, we introduced reciprocal mutations between LN40 and B33 at these critical positions. Methods Three groups of four rabbits were primed with one of three chimeric LN40/B33 gp120 DNAs, followed by a polyvalent protein boost. Time course and endpoint titers were determined via ELISA. Neutralization breadth was analyzed by Monogram against a panel of sixteen viruses using a Phenosense neutralization assay. Anti-gp120 serum specificities were determined using a set of overlapping peptides spanning the entire gp120 via ELISA. Results We found that sera primed with a B33 chimera containing specific LN40 residues within the V3 loop and the CD4 binding loop displayed enhanced neutralization breadth against a cross-clade panel of Tier 1 and 2 viruses compared to the B33-primed group. Interestingly, a second B33 chimera containing two additional LN40 substitutions (Stu-Bsu R373/N386) within C3/V4 primed the broadest response, being broader than even the LN40-primed group. Additionally, peptide ELISAs showed differences in reactivity between priming groups which were most pronounced for the C3/V4 region, suggesting an important role for these regions in modulating serum antibody responses against gp120

Beyond Nanopore Sequencing in Space: Identifying the Unknown

Astronaut Kate Rubins sequenced DNA on the International Space Station (ISS) for the first time in August 2016 (Figure 1A). A 2D sequencing library containing an equal mixture of lambda bacteriophage, Escherichia coli, and Mus musculus was prepared on the ground with a SQK_MAP006 kit and sent to the ISS frozen and loaded into R7.3 flow cells. After a total of 9 on-orbit sequencing runs over 6 months, it was determined that there was no decrease in sequencing performance on-orbit compared to ground controls (1). A total of ~280,000 and ~130,000 reads generated on-orbit and on the ground, respectively, identified 90% of reads that were attributed to 30% lambda bacteriophage, 30% Escherichia coli, and 30% M. musculus (Figure 1B). Extensive bioinformatics analysis determined comparable 2D and 1D read accuracies between flight and ground runs (Figure 1C), and data collected from the ISS were able to construct directed assemblies of E.coli and lambda genomes at 100% and M. musculus mitochondrial genome at 96.7%. These findings validate sequencing as a viable option for potential on-orbit applications such as environmental microbial monitoring and disease diagnosis. Current microbial monitoring of the ISS applies culture-based techniques that provide colony forming unit (CFU) data for air, water, and surface samples. The identity of the cultured microorganisms in unknown until sample return and ground-based analysis, a process that can take up to 60 days. For sequencing to benefit ISS applications, spaceflight-compatible sample preparation techniques are required. Subsequent to the testing of the MinION on-orbit, a sample-to-sequence method was developed using miniPCR and basic pipetting, which was only recently proven to be effective in microgravity. The work presented here details the in- flight sample preparation process and the first application of DNA sequencing on the ISS to identify unknown ISS-derived microorganisms

Isolation and Monitoring of Cleanroom-Associated Microbial Contaminates From Geological Collections

Microbial contamination is of particular interest to geological curation as many microorganisms can change mineral composition and produce compounds used as biosignatures used for the detection of life. Microbial cells can change the mineral composition of rocks through organic acid production and direct enzymatic oxidation/reduction of transition metals. Enzymatic oxidation of iron and manganese can occur at a rate several orders of magnitude faster than under abiotic conditions and produce highly reactive nanoparticle- sized oxides that can react and sorb other metals and organic compounds. Many fungi can also produce organic acids that dissolve and chelate mineral matrices chemically reducing and dissolving rock surfaces. Finally, several common soil-associated bacteria and fungi produce secondary metabolites that contain unusual amino acid analogs and non-ribosomal peptides containing both L- and D- chirality used in characterizing carbonaceous chondrites and the detection of extraterrestrial life

A novel rabbit monoclonal antibody platform to dissect the diverse repertoire of antibody epitopes for HIV-1 Env immunogen design

The majority of available monoclonal antibodies (MAbs) in the current HIV vaccine field are generated from HIV-1-infected people. In contrast, preclinical immunogenicity studies have mainly focused on polyclonal antibody responses in experimental animals. Although rabbits have been widely used for antibody studies, there has been no report of using rabbit MAbs to dissect the specificity of antibody responses for AIDS vaccine development. Here we report on the production of a panel of 12 MAbs from a New Zealand White (NZW) rabbit that was immunized with an HIV-1 JR-FL gp120 DNA prime and protein boost vaccination regimen. These rabbit MAbs recognized a diverse repertoire of envelope (Env) epitopes ranging from the highly immunogenic V3 region to several previously underappreciated epitopes in the C1, C4, and C5 regions. Nine MAbs showed cross-reactivity to gp120s of clades other than clade B. Increased somatic mutation and extended CDR3 were observed with Ig genes of several molecularly cloned rabbit MAbs. Phylogenic tree analysis showed that the heavy chains of MAbs recognizing the same region on gp120 tend to segregate into an independent subtree. At least three rabbit MAbs showed neutralizing activities with various degrees of breadth and potency. The establishment of this rabbit MAb platform will significantly enhance our ability to test optimal designs of Env immunogens to gain a better understanding of the structural specificity and evolution process of Env-specific antibody responses elicited by candidate AIDS vaccines

IgA as a potential candidate for enteric monoclonal antibody therapeutics with improved gastrointestinal stability

Mucosal surfaces of the gastrointestinal tract play an important role in immune homeostasis and defense and may be compromised by enteric disorders or infection. Therapeutic intervention using monoclonal antibody (mAb) offers the potential for treatment with minimal off-target effects as well as the possibility of limited systemic exposure when administered orally. Critically, to achieve efficacy at luminal surfaces, mAb must remain stable and functionally active in the gastrointestinal environment. To better understand the impact of isotype, class, and molecular structure on the intestinal stability of recombinant antibodies, we used an in vitro simulated intestinal fluid (SIF) assay to evaluate a panel of antibody candidates for enteric mAb-based therapeutics. Recombinant IgG1 was the least stable following SIF incubation, while the stability of IgA generally increased upon polymerization, with subtle differences between subclasses. Notably, patterns of variability within and between mAbs suggest that variable regions contribute to mAb stability and potentially mediate mAb susceptibility to proteases. Despite relatively rapid degradation in SIF, mAbs targeting Enterotoxigenic Escherichia coli (ETEC) displayed functional activity following SIF treatment, with SIgA1 showing improved function compared to SIgA2. The results of this study have implications for the design of enteric therapeutics and subsequent selection of lead candidates based upon in vitro intestinal stability assessments