Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using material from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within genera containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. A representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation.     

Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.     

中国树鼩下丘脑视上核和室旁核内加压素能和催产素能神经元的形态计量学分析

采用免疫组织化学ＰＡＰ／ＤＡＮ－镍加强技术和形态计量法研究了中国树鼩下丘脑加压素（ＶＰ）能和催产素（ＯＴ）能视上核主部（ＳＯＮｐ）、视上核交叉后部（ＳＯＮｒ）和室旁核（ＰＶＮ）的平均矢轴长度,ＳＯＮｐ,ＳＯＮｒ和ＰＶＮ内ＶＰ能和ＯＴ能神经元胞体截面积的平均值;ＳＯＮｐ,ＳＯＮｒ和ＰＶＮ的ＶＰ能和ＯＴ能神经元总数;各校团的各个系列节段内ＶＰ能和ＯＴ能神经元的比较计数。发现,ＳＯＮｐ前１／３部分ＯＴ能神经元明显多于ＶＰ能的,而后２／３部分则相反;ＳＯＮｒ前２／３部分ＶＰ能神经元明显多于ＯＴ能的,而后１／３部分两者差别不明显;ＰＶＮ前２／３部分ＯＴ能神经元明显多于ＶＰ能的,而后１／３部分则相反。本文就中国树下丘脑ＳＯＮ和ＰＶＮ内ＶＰ能和ＯＴ能神经元的形态计量学资料与大鼠的进行了比较。     

A genomewide scan for age-related macular degeneration provides evidence for linkage to several chromosomal regions

We report the results of a genomewide scan for age-related macular degeneration (AMD) in 158 multiplex families. AMD classification was based on fundus photography and was assigned a grade ranging from 1 (no disease) to 5 (exudative disease). Genotyping was performed by the National Heart, Lung, and Blood Institute Mammalian Genotyping Service at Marshfield (404 short tandem repeat markers). The sample included 158 families with two or more siblings with AMD, 490 affected individuals, 101 unaffected individuals, and 38 whose affection status was unknown. Relative pairs included 511 affected sibling, 28 avuncular, 53 cousin, 7 grandparent-grandchild, and 9 grand-avuncular pairs. Two-point parametric and multipoint parametric and nonparametric analyses were performed. Maximum two-point LOD scores of 1.0-2.0 were found for markers on chromosomes 1, 2, 8, 10, 14, 15, and 22. Multipoint analyses were consistent with the two-point results for chromosomes 1, 2, 8, 10, and 22 and provided evidence for additional linkage regions on chromosomes 3, 6, 8, 12, 16, and X. Our signals on chromosomes 1q, 6p, and 10q are consistent with some other previously published results. Significant linkage to AMD was found for one marker on chromosome 2, two adjacent markers on chromosome 3, two adjacent markers on chromosome 6, and seven contiguous markers on chromosome 8, with empirical P values of .00001. The consistency of many of the other signals across both two-point and multipoint, as well as parametric and nonparametric, analyses indicate several other regions worthy of follow-up.     

中国树鼩下丘脑视上核和室旁核内加压素和催产素能神经元的比较分布

应用PAP-PAAP双重免疫组化染色程序在同一切片上进行两种肽能物质的定位,观察了中国树鼩下丘脑视上核和室旁核内VP能和OT能神经元的比较解剖学分布,发现:视上核被视束分成主部和交叉后部。在视上核主部,其头侧部几乎仅含OT能神经元胞体,中间部VP能胞体出现并逐渐增多,尾侧部VP能胞体数目明显超过OT能胞体。在明显含有两种胞体的中间部和尾侧部,OT能胞体多位于背内侧,VP能胞体多位于腹外侧;在视上核交叉后部,其头侧部以VP能胞体为主,且多位于背外侧,OT能胞体多位于腹内侧。中间部OT能胞体多位于内侧,VP能胞体多位于外侧。尾侧部OT能胞体多位于背、腹两侧,VP能胞体则多位于中间;在室旁核,其头侧部几乎全由OT能胞体构成。中间部,VP能胞体出现并逐渐增多,OT和VP能胞体分别主要位于内、外侧。尾侧部两种神经元胞体较明显地分为内、外两群,内侧群主要为OT能胞体,外侧群几乎全为VP能胞体,该群的头侧半又可分为背腹两个亚群,至尾侧半,此二亚群渐合并。本文讨论了OT和VP能神经元在中国树鼩和大鼠视上核和室旁核内的比较分布。     

The RAD23 Family Provides an Essential Connection between the 26S Proteasome and Ubiquitylated Proteins in Arabidopsis

The ubiquitin (Ub)/26S proteasome system (UPS) directs the turnover of numerous regulatory proteins, thereby exerting control over many aspects of plant growth, development, and survival. The UPS is directed in part by a group of Ub-like/Ub-associated (UBL/UBA) proteins that help shuttle ubiquitylated proteins to the 26S proteasome for breakdown. Here, we describe the collection of UBL/UBA proteins in Arabidopsis thaliana, including four isoforms that comprise the RADIATION SENSITIVE23 (RAD23) family. The nuclear-enriched RAD23 proteins bind Ub conjugates, especially those linked internally through Lys-48, via their UBA domains, and associate with the 26S proteasome Ub receptor RPN10 via their N-terminal UBL domains. Whereas homozygous mutants individually affecting the four RAD23 genes are without phenotypic consequences (rad23a, rad23c, and rad23d) or induce mild phyllotaxy and sterility defects (rad23b), higher-order mutant combinations generate severely dwarfed plants, with the quadruple mutant displaying reproductive lethality. Both the synergistic effects of a rad23b-1 rpn10-1 combination and the response of rad23b plants to mitomycin C suggest that RAD23b regulates cell division. Taken together, RAD23 proteins appear to play an essential role in the cell cycle, morphology, and fertility of plants through their delivery of UPS substrates to the 26S proteasome.     

Foraging and Calling Behavior of Carolina chickadees (Poecile carolinensis) in Response to the Head Orientation of Potential Predators

When animals detect predators they modify their behavior to avoid predation. However, less is known about whether prey species modify their behavior in response to predator body and behavioral cues. Recent studies indicated that tufted titmice, a small songbird, decreased their foraging behavior and increased their calling rates when they detected a potential predator facing toward a feeder they were using, compared to a potential predator facing away from that feeder. Here, we tested whether related Carolina chickadees, Poecile carolinensis, were also sensitive not just to the presence of a predator model, but to its facial/head orientation. Although chickadees are closely related to titmice, recent studies in different populations suggest chickadees respond to risky contexts involving predators differently than titmice. We conducted two field studies near feeders the birds were exploiting. In Study One, a mask‐wearing human observer stood near the feeder. In Study Two, a model of a domestic cat was positioned near the feeder. In both studies, the potential threatening stimulus either faced toward or faced away from the feeder. Chickadees avoided the feeder more in both studies when the potential predator was present, and showed strongest feeder avoidance when the potential predator faced toward the feeder. Chickadee calling behavior was also affected by the facial orientation of the potential predator in Study 1. These results suggest that, like titmice, chickadees exhibit predation‐risk‐sensitive foraging and calling behavior, in relation to facial and head orientation of potential threats. These small birds seem to attend to the likely visual space of potential predators. Sensitivity to predator cues like behavior and body posture must become more central to our theories and models of anti‐predator behavioral systems.     

Determination of the spread of HIV from the AIDS incidence history

The relation between the incidence of HIV in the general population, the number of AIDS cases, and the incubation period for the disease is examined. The number of AIDS cases can be expressed in terms of a convolution integral over the incubation period distribution and the temporal history of HIV incidence. In order to determine the level of HIV incidence it is necessary to invert the convolution. In this manner, it is possible to determine the spread of HIV up to the present time from knowledge of the AIDS incidence history and the incubation period. We describe the inversion of the convolution in terms of a Laplace transform technique that is applicable for any given incubation period distribution. Substantial simplifications in the technique are found in the case of an Erlang distribution for the probability density. The spread of HIV infections in the United States is charted through 1988 using AIDS incidence data that are corrected for both the revised AIDS case definition and reporting time delays. The results are consistent with current estimates of the HIV incidence in the United States and show no evidence of saturation in the rate of new infections. Indeed, the rate of new infections still appears to be climbing as of that date. While the technique is unable to predict the future course of the epidemic, it may provide a useful benchmark for comparison with mathematical models of the epidemic. The techniques are conceptually applicable to diseases other than AIDS.     

Affinity Purification of the Arabidopsis 26 S Proteasome Reveals a Diverse Array of Plant Proteolytic Complexes

Selective proteolysis in plants is largely mediated by the ubiquitin (Ub)/proteasome system in which substrates, marked by the covalent attachment of Ub, are degraded by the 26 S proteasome. The 26 S proteasome is composed of two subparticles, the 20 S core protease (CP) that compartmentalizes the protease active sites and the 19 S regulatory particle that recognizes and translocates appropriate substrates into the CP lumen for breakdown. Here, we describe an affinity method to rapidly purify epitope-tagged 26 S proteasomes intact from Arabidopsis thaliana. In-depth mass spectrometric analyses of preparations generated from young seedlings confirmed that the 2.5-MDa CP-regulatory particle complex is actually a heterogeneous set of particles assembled with paralogous pairs for most subunits. A number of these subunits are modified post-translationally by proteolytic processing, acetylation, and/or ubiquitylation. Several proteasome-associated proteins were also identified that likely assist in complex assembly and regulation. In addition, we detected a particle consisting of the CP capped by the single subunit PA200 activator that may be involved in Ub-independent protein breakdown. Taken together, it appears that a diverse and highly dynamic population of proteasomes is assembled in plants, which may expand the target specificity and functions of intracellular proteolysis.