Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays

Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5′-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5′ guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5′-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling

Local diversity in settlement, demography and subsistence across the southern Indian Neolithic-Iron Age transition: site growth and abandonment at Sanganakallu-Kupgal

The Southern Indian Neolithic-Iron Age transition demonstrates considerable regional variability in settlement location, density, and size. While researchers have shown that the region around the Tungabhadra and Krishna River basins displays significant subsistence and demographic continuity, and intensification, from the Neolithic into the Iron Age ca. 1200 cal. BC, archaeological and chronometric records in the Sanganakallu region point to hilltop village expansion during the Late Neolithic and ‘Megalithic’ transition period (ca. 1400–1200 cal. BC) prior to apparent abandonment ca. 1200 cal. BC, with little evidence for the introduction of iron technology into the region. We suggest that the difference in these settlement histories is a result of differential access to stable water resources during a period of weakening and fluctuating monsoon across a generally arid landscape. Here, we describe well-dated, integrated chronological, archaeobotanical, archaeozoological and archaeological survey datasets from the Sanganakallu-Kupgal site complex that together demonstrate an intensification of settlement, subsistence and craft production on local hilltops prior to almost complete abandonment ca. 1200 cal. BC. Although the southern Deccan region as a whole may have witnessed demographic increase, as well as subsistence and cultural continuity, at this time, this broader pattern of continuity and resilience is punctuated by local examples of abandonment and mobility driven by an increasing practical and political concern with water

In Search of Cellular Immunophenotypes in the Blood of Children with Autism

Autism is a neurodevelopmental disorder characterized by impairments in social behavior, communication difficulties and the occurrence of repetitive or stereotyped behaviors. There has been substantial evidence for dysregulation of the immune system in autism.We evaluated differences in the number and phenotype of circulating blood cells in young children with autism (n = 70) compared with age-matched controls (n = 35). Children with a confirmed diagnosis of autism (4-6 years of age) were further subdivided into low (IQ<68, n = 35) or high functioning (IQ ≥ 68, n = 35) groups. Age- and gender-matched typically developing children constituted the control group. Six hundred and forty four primary and secondary variables, including cell counts and the abundance of cell surface antigens, were assessed using microvolume laser scanning cytometry.There were multiple differences in immune cell populations between the autism and control groups. The absolute number of B cells per volume of blood was over 20% higher for children with autism and the absolute number of NK cells was about 40% higher. Neither of these variables showed significant difference between the low and high functioning autism groups. While the absolute number of T cells was not different across groups, a number of cellular activation markers, including HLA-DR and CD26 on T cells, and CD38 on B cells, were significantly higher in the autism group compared to controls.These results support previous findings that immune dysfunction may occur in some children with autism. Further evaluation of the nature of the dysfunction and how it may play a role in the etiology of autism or in facets of autism neuropathology and/or behavior are needed