Coherent two-dimensional nanoscopy

We introduce a spectroscopic method that determines nonlinear quantum mechanical response functions beyond the optical diffraction limit and allows direct imaging of nanoscale coherence. In established coherent two-dimensional (2D) spectroscopy, four-wave-mixing responses are measured using three ingoing waves and one outgoing wave; thus, the method is diffraction-limited in spatial resolution. In coherent 2D nanoscopy, we use four ingoing waves and detect the final state via photoemission electron microscopy, which has 50-nanometer spatial resolution. We recorded local nanospectra from a corrugated silver surface and observed subwavelength 2D line shape variations. Plasmonic phase coherence of localized excitations persisted for about 100 femtoseconds and exhibited coherent beats. The observations are best explained by a model in which coupled oscillators lead to Fano-like resonances in the hybridized dark- and bright-mode response.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Immunologic manipulation of metastases due to herpesvirus transformed cells

Herpes simplex virus type 1 (HSV-1), type 2 (HSV-2), and simian virus 40 (SV40) fail to induce immunity in weanling Syrian hamsters to transplant of hamster cells transformed by HSV-2. However, the development of metastatic tumors is markedly enhanced by prior immunization with HSV-1. Immunization with SV40, ultraviolet-irradiated tumor cells, or ultraviolet-irradiated normal hamster embryo cells inhibits the development of metastases. The HSV-hamster system appears a good one for the study of development, prevention, and control of metastases by mammalian cells transformed by a common human virus.     

GFAJ-1 is an arsenate-resistant, phosphate-dependent organism

The bacterial isolate GFAJ-1 has been proposed to substitute arsenic for phosphorus to sustain growth. We have shown that GFAJ-1 is able to grow at low phosphate concentrations (1.7 μM), even in the presence of high concentrations of arsenate (40 mM), but lacks the ability to grow in phosphorus-depleted (<0.3 μM), arsenate-containing medium. High-resolution mass spectrometry analyses revealed that phosphorylated central metabolites and phosphorylated nucleic acids predominated. A few arsenylated compounds, including C6 sugar arsenates, were detected in extracts of GFAJ-1, when GFAJ-1 was incubated with arsenate, but further experiments showed they formed abiotically. Inductively coupled plasma mass spectrometry confirmed the presence of phosphorus in nucleic acid extracts, while arsenic could not be detected and was below 1 per mil relative to phosphorus. Taken together, we conclude that GFAJ-1 is an arsenate-resistant, but still a phosphate-dependent, bacterium.     

Endocranial features of Australopithecus africanus revealed by 2- and 3-D computed tomography

The earliest hominid from South Africa, Australopithecus africanus, is known from only six specimens in which accurate assessment of endocranial capacity and cranial venous outflow pattern can be obtained. This places a severe limit on a number of hypotheses concerning early hominid evolution, particularly those involving brain-body size relationships and adaptations of the circulatory system to evolving upright posture. Advances in high-resolution two- and three-dimensional computed tomography (CT) now allow the inclusion of another important specimen to this list, MLD 37/38 from Makapansgat. A new computer imaging technique is described that "reconstructs" the missing portions of the endocranial cavity in order to determine endocranial capacity. In addition, CT evaluation allows assessment of cranial venous outflow pattern even in cases where the endocranial cavity is completely filled with stone matrix. Results show that endocranial capacity in this specimen is less than originally proposed and also support the view that gracile and robust australopithecines evolved different cranial venous outflow patterns in response to upright postures.     

Assessment of plastic ingestion by pole-caught pelagic predatory fish from O'ahu,Hawai'i

1. Although the frequency of occurrence of plastic ingestion in the large-sized dolphinfish and tunas taken by the Hawai'i longline fishery is very low (frequency of occurrence < 5% of sampled individuals), the ingestion of plastic in smaller-sized specimens caught with pole-and-line gear by commercial and recreational fishers has not been investigated.
2. This study examined ingestion of >0.25 mm marine plastic debris (MPD) by four predatory fish species caught by commercial fishers around the Main Hawaiian Islands, and documented ingestion in three species: 85.7% of albacore tuna (n = 7), 40.0% of skipjack tuna (n = 10) and 12.5% of dolphinfish (n = 8).
3. Yellowfin tuna (n = 10) did not contain any MPD, probably owing to the high proportion of empty stomachs (60%).
4. For skipjack tuna, the frequency of occurrence of MPD ingestion was significantly higher for the smaller-sized specimens caught with pole-and-line (40%), compared with the larger-sized specimens caught with longlines (0%).
5. For dolphinfish, the frequency of occurrence of MPD ingestion was similar for the similar-sized specimens caught with pole-and-line and with longlines.
6. The ingested MPD items were micro–meso plastics, between 1 and 25 mm. While most ingested items were fragments, albacore also ingested line and skipjack also ingested sheets.
7. The predatory fishes ingested light MPD items that float in sea water, but there were species-specific differences in their polymer composition: albacore contained more polypropylene and polyethylene, and skipjack contained more elastomers, characterized by a high percentage of ester plasticizers.
8. Altogether, these results suggest that albacore and skipjack tunas ingest plastic of different types and polymers. Yet more research is needed to understand how differences in vertical distribution, foraging ecology and diet influence the MPD sampled by these predatory fish species.

     

Effects of salinity on osmoregulation,growth and survival in Asian swamp eel (Monopterus albus) (Zuiew 1793)

The Asian swamp eel Monopterus albus is normally considered a freshwater species, but can also occasionally be found in brackish water. It is an obligate air‐breather with highly reduced gills, making its osmoregulation physiology interesting because the gills normally represent the primary site of osmoregulation in teleosts. Being a popular fish for human consumption, the swamp eel is cultured extensively in freshwater ponds in the Mekong Delta of Vietnam. However, very little is known about its salinity tolerance, which is becoming topical due to the increasing salt‐water intrusions into tropical deltas. We therefore studied how increased salinity affects survival, growth, blood pressure, heart rate, blood osmolality and plasma ions. All eels survived prolonged exposure to 5 and 10 g L^?1, although plasma osmolality increased significantly at 10 g L^?1. Further elevation to 15 and 20 g L^?1 was associated with significantly elevated mortality, with a corresponding increase in plasma osmolality and ion con‐centrations. Our results show that swamp eels thrive in 0–10 g L^?1 with an optimum growth between 0 and 9 g L^?1, indicating that utilization of low saline brackish waters for aquaculture is possible.     

Genome streamlining in a cosmopolitan oceanic bacterium

The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.     

Rapid chemically induced changes of PtdIns(4,5)P2 gate KCNQ ion channels

To resolve the controversy about messengers regulating KCNQ ion channels during phospholipase C-mediated suppression of current, we designed translocatable enzymes that quickly alter the phosphoinositide composition of the plasma membrane after application of a chemical cue. The KCNQ current falls rapidly to zero when phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2 or PI(4,5)P2] is depleted without changing Ca2+, diacylglycerol, or inositol 1,4,5-trisphosphate. Current rises by 30% when PI(4,5)P2 is overproduced and does not change when phosphatidylinositol 3,4,5-trisphosphate is raised. Hence, the depletion of PI(4,5)P2 suffices to suppress current fully, and other second messengers are not needed. Our approach is ideally suited to study biological signaling networks involving membrane phosphoinositides.