Predators alter the scaling of diversity in prey metacommunities

Although predator effects on the number of locally coexisting species are well understood, there are few formal predictions of how these local predator effects influence patterns of prey diversity at larger spatial scales. Building on the theory of island biogeography, we develop a simple model that describes how predators can alter the scaling of diversity in prey metacommunities and compares the effects of generalist and specialist predators on regional prey diversity. Generalist predators, which consume prey randomly with respect to species identity, are predicted to reduce α‐diversity and increase β‐diversity thereby maintaining regional diversity (γ‐diversity). Alternatively, specialist predators, which filter out prey species intolerant of predators, are predicted to reduce bothα‐diversity andβ‐diversity by causing the same prey species to be extirpated in each locality, resulting in regional prey species extinctions and lower γ‐diversity. These distinct effects of generalist and specialist predators on prey diversity at different spatial scales are uniquely shaped by the extent of predation within those metacommunities. Overall, our model results make general predictions for how different types of predators can differentially affect prey diversity across spatial scales, allowing a more complete understanding of the possible implications of predator eradications or introductions for biodiversity.     

Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity

The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESCs) and has been implicated in mESC maintenance. Here we demonstrate that, unlike genetic deletion, RNAi-mediated depletion of Tet1 in mESCs led to a significant reduction in 5hmC and loss of mESC identity. The differentiation phenotype due to Tet1 depletion positively correlated with the extent of 5hmC loss. Meta-analyses of genomic data sets suggested interaction between Tet1 and leukemia inhibitory factor (LIF) signaling. LIF signaling is known to promote self-renewal and pluripotency in mESCs partly by opposing MAPK/ERK-mediated differentiation. Withdrawal of LIF leads to differentiation of mESCs. We discovered that Tet1 depletion impaired LIF-dependent Stat3-mediated gene activation by affecting Stat3's ability to bind to its target sites on chromatin. Nanog overexpression or inhibition of MAPK/ERK signaling, both known to maintain mESCs in the absence of LIF, rescued Tet1 depletion, further supporting the dependence of LIF/Stat3 signaling on Tet1. These data support the conclusion that analysis of mESCs in the hours/days immediately following efficient Tet1 depletion reveals Tet1's normal physiological role in maintaining the pluripotent state that may be subject to homeostatic compensation in genetic models.     

Human tRNA genes function as chromatin insulators

Insulators help separate active chromatin domains from silenced ones. In yeast, gene promoters act as insulators to block the spread of Sir and HP1 mediated silencing while in metazoans most insulators are multipartite autonomous entities. tDNAs are repetitive sequences dispersed throughout the human genome and we now show that some of these tDNAs can function as insulators in human cells. Using computational methods, we identified putative human tDNA insulators. Using silencer blocking, transgene protection and repressor blocking assays we show that some of these tDNA-containing fragments can function as barrier insulators in human cells. We find that these elements also have the ability to block enhancers from activating RNA pol II transcribed promoters. Characterization of a putative tDNA insulator in human cells reveals that the site possesses chromatin signatures similar to those observed at other better-characterized eukaryotic insulators. Enhanced 4C analysis demonstrates that the tDNA insulator makes long-range chromatin contacts with other tDNAs and ETC sites but not with intervening or flanking RNA pol II transcribed genes.     

Southeastern U.S.A. continental shelf respiratory rates revisited

Respiratory rates on the U. S. southeastern continental shelf have been estimated several times by different investigators, most recently by Jiang et al. (Biogeochemistry 98:101–113, 2010) who report lower mean rates than were found in earlier work and attribute the differences to analytical error in all methods used in earlier studies. The differences are, instead, attributable to the differences in the geographical scope of the studies. The lower estimates of regional organic carbon flux of Jiang et al. (Biogeochemistry 98:101–113, 2010) are a consequence of their extrapolation of data from a small portion of the shelf to the entire South Atlantic Bight. This comment examines the methodologies used as well as the variability of respiratory rates in this region over space and time.     

Chimeric relaxin peptides highlight the role of the A-chain in the function of H2 relaxin

Human gene-2 (H2) relaxin is a member of the insulin-relaxin peptide superfamily. Because of the potential clinical applications of H2 relaxin, there is a need for novel analogs that have improved biological activity and receptor specificity. In this respect, we have chemically assembled chimeric peptides consisting of the B-chain of H2 relaxin in combination with A-chains from other insulin/relaxin family members. The peptides were prepared using solid phase peptide synthesis together with regioselective disulfide bond formation and characterized by RP-HPLC, MALDI-TOF MS and amino acid analysis. Their in vitro activity was assessed in RXFP1 or RXFP2 expressing cells. Replacement of the H2 relaxin A-chain resulted in parallel losses of binding affinity and activity on RXFP1. Not surprisingly H1A-H2B demonstrated the highest activity as the H1 A-chain shares high homology with H2 relaxin whereas INSLA-H2B, which shows low homology, had very poor activity. Importantly A-chain replacements had a dramatic effect on RXFP2 activity similar to previous results demonstrating different modes of activation of A-chain variants on RXFP1 and RXFP2. H3A-H2B is particularly interesting as it displays moderate activity at RXFP1 but poor activity at RXFP2 indicating that it may be a template for specific RXFP1 agonist development. Our study confirms that the activity of H2 relaxin at both RXFP1 and RXFP2 relies on interactions with both the B- and A-chains, and also provide new biochemical insights into the mechanism of relaxin action that the A-chain needs to be in native or near-native form for strong RXFP1 or RXFP2 agonist activity.     

Affinity-purification coupled to mass spectrometry: basic principles and strategies

Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.     

Short-term presynaptic plasticity

Different types of synapses are specialized to interpret spike trains in their own way by virtue of the complement of short-term synaptic plasticity mechanisms they possess. Numerous types of short-term, use-dependent synaptic plasticity regulate neurotransmitter release. Short-term depression is prominent after a single conditioning stimulus and recovers in seconds. Sustained presynaptic activation can result in more profound depression that recovers more slowly. An enhancement of release known as facilitation is prominent after single conditioning stimuli and lasts for hundreds of milliseconds. Finally, tetanic activation can enhance synaptic strength for tens of seconds to minutes through processes known as augmentation and posttetantic potentiation. Progress in clarifying the properties, mechanisms, and functional roles of these forms of short-term plasticity is reviewed here.     

Rapid Development of Resistance of Wounds on Immature Apricot Fruit to Infection with Monilinia fructicola

Cleanly cut wounds on the surface of green apricot fruit are susceptible to infection with Monilinia fructicola when freshly made, but rapidly become resistant over 6 h. This was shown to be strongly correlated with the concentration of free nutrients, particularly sugars, which remain on the surface of the wound. Nutrients were rapidly removed by diffusion and absorption by underlying living cells. This is proposed as the basis of resistance which develops rapidly as the wounds age. Structural and chemical barriers to infection, such as periderm, suberin and phenolic compounds, developed long after the wounds had become resistant.