Persisting viral sequences shape microbial CRISPR-based immunity

Well-studied innate immune systems exist throughout bacteria and archaea, but a more recently discovered genomic locus may offer prokaryotes surprising immunological adaptability. Mediated by a cassette-like genomic locus termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), the microbial adaptive immune system differs from its eukaryotic immune analogues by incorporating new immunities unidirectionally. CRISPR thus stores genomically recoverable timelines of virus-host coevolution in natural organisms refractory to laboratory cultivation. Here we combined a population genetic mathematical model of CRISPR-virus coevolution with six years of metagenomic sequencing to link the recoverable genomic dynamics of CRISPR loci to the unknown population dynamics of virus and host in natural communities. Metagenomic reconstructions in an acid-mine drainage system document CRISPR loci conserving ancestral immune elements to the base-pair across thousands of microbial generations. This 'trailer-end conservation' occurs despite rapid viral mutation and despite rapid prokaryotic genomic deletion. The trailer-ends of many reconstructed CRISPR loci are also largely identical across a population. 'Trailer-end clonality' occurs despite predictions of host immunological diversity due to negative frequency dependent selection (kill the winner dynamics). Statistical clustering and model simulations explain this lack of diversity by capturing rapid selective sweeps by highly immune CRISPR lineages. Potentially explaining 'trailer-end conservation,' we record the first example of a viral bloom overwhelming a CRISPR system. The polyclonal viruses bloom even though they share sequences previously targeted by host CRISPR loci. Simulations show how increasing random genomic deletions in CRISPR loci purges immunological controls on long-lived viral sequences, allowing polyclonal viruses to bloom and depressing host fitness. Our results thus link documented patterns of genomic conservation in CRISPR loci to an evolutionary advantage against persistent viruses. By maintaining old immunities, selection may be tuning CRISPR-mediated immunity against viruses reemerging from lysogeny or migration.     

Genomic features of lactic acid bacteria effecting bioprocessing and health

The lactic acid bacteria are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. More recently, selected members of the lactic acid bacteria have been implicated in a number of probiotic roles that impact general health and well-being. Genomic analyses of multiple members of the lactic acid bacteria, at the genus, species, and strain level, have now elucidated many genetic features that direct their fermentative and probiotic roles. This information is providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes and, in some cases, potentially underlying probiotic activities within complex microbial and host ecosystems.     

Annual cycle and diversity of species and infraspecific taxa of Ceratium (Dinophyceae) in the Ligurian Sea,northwest Mediterranean1

We examined the well‐documented and species‐rich dinoflagellate genus Ceratium Schrank in the northwest Mediterranean Sea as a possible model for marine phytoplankton diversity and as a biological indicator of global climate change. First, we investigated the influence of counting effort; we then documented temporal changes in Ceratium specific and infraspecific taxa over 2 years (2002 and 2003) in the Villefranche Bay based on a monthly net sampling. Finally, we tried to identify factors associated with shifts in biodiversity. The calculation of taxonomic diversity, regularity, and richness were highly dependent on counting effort. We determined that a minimal sample volume of ～70 L was needed to obtain a good estimation of species richness. The annual cycle was characterized by a seasonal trend of high winter species richness followed by low spring biodiversity. Infraspecific variability not only appeared to depend on water temperature but also seemed to be influenced by bottom‐up control and was strongly affected by top‐down control. Thus, the occurrence of high concentrations of salps (Thalia democratica) and copepods larger than 2 mm (Calanus helgolandicus) coincided with a drastic decrease of Ceratium abundance and diversity during spring 2003. Ceratium is sensitive to both abiotic and biotic factors and could prove to be a good candidate as a biological indicator of global change.     

Conversion of orally administered 2-n.pentylaminoacetamide into glycinamide and glycine in the rat brain

Male Sprague Dawley albino rats were treated orally with 2-n.pentylaminoacetamide (10 to 100 mg/kg b.wt). This oral administration provoked a dose-related and time-dependent accumulation of glycinamide in forebrain, cerebellum, and medulla, and to increased levels of glycine in the three brain areas, and of serine in medulla. In kidney, liver and plasma, the accumulation of glycinamide was lower and there was no increase in glycine and serine levels. With a dose of 100 mg/kg b.wt, 28% of the drug were eliminated unchanged and 16% as glycinamide, in urines collected for 24 h. In all tissues examined, 2-n.pentylaminoacetamide and glycinamide levels peaked at 1 h and were nil again after 24 h, the ratio of 2-n.pentylaminoacetamide over glycinamide decreasing more rapidly in brain than in kidney and liver. Contrasting with the effects of 2-n.pentylaminoacetamide, the oral administration of glycinamide (66 mg/b.wt) led, 2 hours later, to similar low rises of glycinamide in plasma and brain. In another control experiment, the intraperitoneal injection of a large dose of glycine (450 mg/kg b.wt) provoked, 30 min later, modest rises of glycine levels in the central nervous system that merely reflected a contamination by plasma glycine.     

Structural and Evolutionary Relationships Among Chitinases of Flowering Plants

The analysis of nuclear-encoded chitinase sequences from various angiosperms has allowed the categorization of the chitinases into discrete classes. Nucleotide sequences of their catalytic domains were compared in this study to investigate the evolutionary relationships between chitinase classes. The functionally distinct class III chitinases appear to be more closely related to fungal enzymes involved in morphogenesis than to other plant chitinases. The ordering of other plant chitinases into additional classes mainly relied on the presence of auxiliary domains—namely, a chitin-binding domain and a carboxy-terminal extension—flanking the main catalytic domain. The results of our phylogenetic analyses showed that classes I and IV form discrete and well-supported monophyletic groups derived from a common ancestral sequence that predates the divergence of dicots and monocots. In contrast, other sequences included in classes I* and II, lacking one or both types of auxiliary domains, were nested within class I sequences, indicating that they have a polyphyletic origin. According to phylogenetic analyses and the calculation of evolutionary rates, these chitinases probably arose from different class I lineages by relatively recent deletion events. The occurrence of such evolutionary trends in cultivated plants and their potential involvement in host–pathogen interactions are discussed. Received: 5 July 1996 / Accepted: 9 January 1997     

Morphology and Molecules Reveal Unexpected Cryptic Diversity in the Enigmatic Genus Sinobirma Bryk, 1944 (Lepidoptera: Saturniidae)

The wild silkmoth genus Sinobirma Bryk, 1944 is a poorly known monotypic taxon from the eastern end of the Himalaya Range. It was convincingly proposed to be closely related to some members of an exclusively Afro-tropical group of Saturniidae, but its biogeographical and evolutionary history remains enigmatic. After examining recently collected material from Tibet, northern India, and northeastern Myanmar, we realized that this unique species, S. malaisei Bryk, 1944 only known so far from a few specimens and from a very restricted area near the border between north-eastern Myanmar and the Yunnan province of China, may in fact belong to a group of closely related cryptic species. In this work, we combined morphological comparative study, DNA barcoding, and the sequences of a nuclear marker (D2 expansion segment of the 28S rRNA gene) to unequivocally delimit three distinct species in the genus Sinobirma, of which two are described as new to science: S. myanmarensis sp. n. and S. bouyeri sp. n. An informative DNA barcode sequence was obtained from the female holotype of S. malaisei—collected in 1934—ensuring the proper assignation of this name to the newly collected and studied specimens. Our findings represent another example of the potential of coupling traditional taxonomy and DNA barcoding for revealing and solving difficult cases of cryptic diversity. This approach is now being generalized to the world fauna of Saturniidae, with the participation of most of the taxonomists studying these moths.     

Joint Modeling of the Clinical Progression and of the Biomarkers' Dynamics Using a Mechanistic Model

Summary Joint models are used to rigorously explore the relationship between the dynamics of biomarkers and clinical events. In the context of HIV infection, where the multivariate dynamics of HIV‐RNA and CD4 are complex, a mechanistic approach based on a system of nonlinear differential equations naturally takes into account the correlation between the biomarkers. Using data from a randomized clinical trial comparing dual antiretroviral therapy to a single drug regimen, a full maximum likelihood approach is proposed to explore the relationship between the evolution of the biomarkers and the time to a clinical event. The role of each marker as an independent predictor of disease progression is assessed. We show that the joint dynamics of HIV‐RNA and CD4 captures the effect of antiretroviral treatment; the CD4 dynamics alone is found to capture most but not all of the treatment effect.     

Cell intrinsic TGF-beta 1 regulation of B cells

TGF-beta family cytokines play multiple roles in immune responses. TGF-beta1-null mice suffer from multi-organ infiltration that leads to their premature death. T cells play a central role in the TGF-beta1 phenotype, as deficiency of TGF-beta1 only in T cells reproduces the lethal phenotype. Although it is known that TGF-beta1 controls B cells isotype switch and homeostasis, the source responsible for this control has not been characterized. Because of the major role that T cells play in regulating B cell responses, we addressed the T cell dependency of the TGF-beta1 control of B cells. The analysis of T cell-deficient, TGF-beta1 knockout mice and the production of chimeras in which B but not T cells lacked TGF-beta1 allowed us to show that B cells are controlled in part by cell autonomous production of TGF-beta1.