Accumulation and local proliferation of antigen-specific CD4+ T cells in antigen-bearing tissue

Although activation and subsequent expansion of naive CD4(+) T cells within lymph nodes is well characterized, the fate of T effector cells activated within peripheral tissues during secondary reactions is poorly defined. Therefore, we studied the recruitment, proliferation and egress of antigen-specific Th1 effector cells in comparison with nonspecific Th1 cells throughout a delayed-type hypersensitivity reaction (DTH). Although we observed a high turnover of Th1 effector cells with unspecific high-rate recruitment and CCR7-dependent egress from the inflamed tissue in the early, acute DTH phase, a strong, selective accumulation of antigen-specific T cells occurred during the chronic, late DTH phase. This was mainly based on local proliferation of CD4(+) effector cells within the DTH tissue and concomitant retention. Considering the strong CCR7-dependent Th cell egress found in this model, the reduced CCR7 expression on antigen-specific T cells isolated from late-phase DTH tissue most likely contributes to the retention of these cells within the tissue. Thus, peripheral tissues can support not only the proliferation of CD8(+) T cells, as recently shown, but also that of CD4(+) T effector cells, forming a pool of tissue-resident T cells.     

Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease

Although the causes of Parkinson's disease (PD) are thought to be primarily environmental, recent studies suggest that a number of genes influence susceptibility. Using targeted case recruitment and online survey instruments, we conducted the largest case-control genome-wide association study (GWAS) of PD based on a single collection of individuals to date (3,426 cases and 29,624 controls). We discovered two novel, genome-wide significant associations with PD-rs6812193 near SCARB2 (p = 7.6 × 10(-10), OR = 0.84) and rs11868035 near SREBF1/RAI1 (p = 5.6 × 10(-8), OR = 0.85)-both replicated in an independent cohort. We also replicated 20 previously discovered genetic associations (including LRRK2, GBA, SNCA, MAPT, GAK, and the HLA region), providing support for our novel study design. Relying on a recently proposed method based on genome-wide sharing estimates between distantly related individuals, we estimated the heritability of PD to be at least 0.27. Finally, using sparse regression techniques, we constructed predictive models that account for 6%-7% of the total variance in liability and that suggest the presence of true associations just beyond genome-wide significance, as confirmed through both internal and external cross-validation. These results indicate a substantial, but by no means total, contribution of genetics underlying susceptibility to both early-onset and late-onset PD, suggesting that, despite the novel associations discovered here and elsewhere, the majority of the genetic component for Parkinson's disease remains to be discovered.     

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

MOTIVATION: Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses. RESULTS: In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.     

The filopodium: A stable structure with highly regulated repetitive cycles of elongation and persistence depending on the actin cross-linker fascin

The ability of mammalian cells to adhere and to migrate is an essential prerequisite to form higher organisms. Early migratory events include substrate sensing, adhesion formation, actin bundle assembly and force generation. Latest research revealed that filopodia are important not only for sensing the substrate but for all of the aforementioned highly regulated processes. However, the exact regulatory mechanisms are still barely understood. Here, we demonstrate that filopodia of human keratinocytes exhibit distinct cycles of repetitive elongation and persistence. A single filopodium thereby is able to initiate the formation of several stable adhesions. Every single filopodial cycle is characterized by an elongation phase, followed by a stabilization time and in many cases a persistence phase. The whole process is strongly connected to the velocity of the lamellipodial leading edge, characterized by a similar phase behavior with a slight time shift compared with filopodia and a different velocity. Most importantly, re-growth of existing filopodia is induced at a sharply defined distance between the filopodial tip and the lamellipodial leading edge. On the molecular level this regrowth is preceded by a strong filopodial reduction of the actin bundling protein fascin. This reduction is achieved by a switch to actin polymerization without fascin incorporation at the filopodial tip and therefore subsequent out-transport of the cross-linker by actin retrograde flow.Key words: filopodia, lamellipodia, cell migration, fascin, adhesion, retrograde flow, actin polymerization     

In vivo differentiated cytokine-producing CD4(+) T cells express functional CCR7

Chemokines and their receptors fulfill specialized roles in inflammation and under homeostatic conditions. CCR7 and its ligands, CCL19 and CCL21, are involved in lymphocyte recirculation through secondary lymphoid organs and additionally navigate lymphocytes into distinct tissue compartments. The role of CCR7 in the migration of polarized T effector/memory cell subsets in vivo is still poorly understood. We therefore analyzed murine and human CD4(+) cytokine-producing cells developed in vivo for their chemotactic reactivity to CCR7 ligands. The responses of cells producing cytokines, such as IFN-gamma, IL-4, and IL-10, as well as of subsets defined by memory or activation markers were comparable to that of naive CD4(+) cells, with slightly lower reactivity in cells expressing IL-10 or CD69. This indicates that CCR7 ligands are able to attract naive as well as the vast majority of activated and effector/memory T cell stages. Chemotactic reactivity of these cells toward CCL21 was absent in CCR7-deficient cells, proving that effector cells do not use alternative receptors for this chemokine. Th1 cells generated from CCR7(-/-) mice failed to enter lymph nodes and Peyer's patches, but did enter a site of inflammation. These findings indicate that CD4(+) cells producing effector cytokines upon stimulation retain the capacity to recirculate through lymphoid tissues via CCR7.     

Simulating effects of climate change under direct and diapause development in a butterfly

Temperature is one of the most important ecological factors affecting species survival and distributions. Therefore, global climate change, involving increases in mean surface temperature and the occurrence of extreme weather events, may pose a substantial challenge to biodiversity. Whereas tropical ectotherms are believed to be very sensitive to climate change, temperate‐zone species may actually benefit from higher temperatures. However, as in temperate zones large parts of the year are unsuitable for growth and reproduction, seasonal time constraints may complicate matters. Against this background we here investigate the impact of simulated climate change, involving increased mean temperatures and heat waves, across developmental pathways of the butterfly Lycaena tityrus (Poda) (Lepidoptera: Lycaenidae). Increased temperatures speeded up development but decreased pupal mass as expected. However, we found no evidence for detrimental effects of increased temperatures or even simulated heat waves. Furthermore, patterns did not differ between indirectly and directly developing individuals, which are assumed to be more time constrained. Our findings support the notion that not all species will be detrimentally affected by climate change, and suggest that species attributes may be more important than potential time constraints imposed by different developmental pathways.     

The Biological Significance of the Pair-bond in the Shrimp Hymenocera picta

The painted shrimp exhibits a social system of “relative monogamy”. The selective consequences of mate attachment for the individuals have been studied by long term observations and experiments.