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Objectives: Many nonhuman primate diets are dominated by plant foods, yet plant tissues are often poor sources of sodium-a necessary mineral for metabolism and health. Among primates, chimpanzees (Pan troglodytes), which are ripe fruit specialists, consume diverse animal, and plant resources. Insects have been proposed as a source of dietary sodium for chimpanzees, yet published data on sodium values for specific foods are limited. We assayed plants and insects commonly eaten by chimpanzees to assess their relative value as sodium sources., Materials and Methods: We used atomic absorption spectroscopy to determine sodium content of key plant foods and insects consumed by chimpanzees of Gombe National Park, Tanzania. Dietary contributions of plant and insect foods were calculated using feeding observational data., Results: On a dry matter basis, mean sodium value of plant foods (n = 83 samples; mean = 86 ppm, SD = 92 ppm) was significantly lower than insects (n = 12; mean = 1549 ppm, SD = 807 ppm) (Wilcoxon rank sum test: W = 975, p < 0.001). All plant values were below the suggested sodium requirement (2000 ppm) for captive primates. While values of assayed insects were variable, sodium content of two commonly consumed insect prey for Gombe chimpanzees (Macrotermes soldiers and Dorylus ants) were four to five times greater than the highest plant values and likely meet requirements., Discussion: We conclude that plant foods available to Gombe chimpanzees are generally poor sources of sodium while insects are important, perhaps critical, sources of sodium for this population., (© 2024 Wiley Periodicals LLC.)

Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics., Competing Interests: The authors declare none., (© The Author(s) 2024.)

Plants depend on the combined action of a shoot-root-soil system to maintain their anchorage to the soil. Mechanical failure of any component of this system results in lodging, a permanent and irreversible inability to maintain vertical orientation. Models of anchorage in grass crops identify the compressive strength of roots near the soil surface as key determinant of resistance to lodging. Indeed, studies of disparate grasses report a ring of thickened, sclerenchyma cells surrounding the root cortex, present only at the base of nodal roots. Here, in the investigation of the development and regulation of this agronomically important trait, we show that development of these cells is uncoupled from the maturation of other secondary cell wall-fortified cells, and that cortical sclerenchyma wall thickening is stimulated by mechanical forces transduced from the shoot to the root. We also show that exogenous application of gibberellic acid stimulates thickening of lignified cell types in the root, including cortical sclerenchyma, but is not sufficient to establish sclerenchyma identity in cortex cells. Leveraging the ability to manipulate cortex development via mechanical stimulus, we show that cortical sclerenchyma development alters root mechanical properties and improves resistance to lodging. We describe transcriptome changes associated with cortical sclerenchyma development under both ambient and mechanically stimulated conditions and identify SECONDARY WALL NAC7 as a putative regulator of mechanically responsive cortex cell wall development at the root base., Competing Interests: CONFLICT OF INTEREST None

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology., Competing Interests: Conflict of interest statement. The authors declare no competing conflicts of interest, financial, or otherwise., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we presented a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops., (© 2022 John Wiley & Sons Ltd.)

Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. We interrogated the genome-wide distribution pattern of mono- and trimethylated histone H3 lysine 4 (H3K4) using chromatin-immunoprecipitation followed by deep-sequencing (ChIP-seq) during key phases of the Chlamydomonas cell cycle: early G 1 phase, Zeitgeber Time 1 (ZT1), when cells initiate biomass accumulation, S/M phase (ZT13) when cells are replicating DNA and undergoing mitosis, and late G 0 phase (ZT23) when they are quiescent. Tri-methylated H3K4 was predominantly enriched at transcription start sites of the majority of protein coding genes (85%). The likelihood of a gene being marked by H3K4me3 correlated with it being transcribed at some point during the life cycle but not necessarily by continuous active transcription, as exemplified by early zygotic genes, which may remain transcriptionally dormant for thousands of generations between sexual cycles. The exceptions to this rule were around 120 loci, some of which encode non-poly-adenylated transcripts, such as small nuclear RNAs and replication-dependent histones that had H3K4me3 peaks only when they were being transcribed. Mono-methylated H3K4 was the default state for the vast majority of histones that were bound outside of transcription start sites and terminator regions of genes. A small fraction of the genome that was depleted of any H3 lysine 4 methylation was enriched for DNA cytosine methylation and the genes within these DNA methylation islands were poorly expressed. Besides marking protein coding genes, H3K4me3 ChIP-seq data served also as a annotation tool for validation of hundreds of long non-coding RNA genes., (© 2022 Society for Experimental Biology and John Wiley & Sons Ltd.)

The eukaryotic green alga Chromochloris zofingiensis is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome-wide histone modification patterns and transcription factor-binding sites alike. Here, we established a ChIP-Seq framework for Chr. zofingiensis yielding over 20 million high-quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250 bp and assessment of the recommended formaldehyde concentration for optimal DNA-protein cross-linking. We used this ChIP-Seq framework to generate a genome-wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA-Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP-Seq data will pave the way for improved genome structural annotation in the emerging reference alga Chr. zofingiensis ., Competing Interests: The authors have no conflicts of interest to declare., (© 2022 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd.)

ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, up-regulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6 -null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels., Competing Interests: The authors declare no competing interest., (Copyright © 2022 the Author(s). Published by PNAS.)

Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a high-throughput approach for characterizing TF-target gene interactions across species and its application to 354 TFs across 48 bacteria, generating 17,000 genome-wide binding maps. This dataset revealed themes of ancient conservation and rapid evolution of regulatory modules. We observed rewiring, where the TF sensing and regulatory role is maintained while the arrangement and identity of target genes diverges, in some cases encoding entirely new functions. We further integrated phenotypic information to define new functional regulatory modules and pathways. Finally, we identified 242 new TF DNA binding motifs, including a 70% increase of known Escherichia coli motifs and the first annotation in Pseudomonas simiae, revealing deep conservation in bacterial promoter architecture. Our method provides a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes., (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts., (© 2021. The Author(s).)

Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur-responsive genes. The CYS-3 transcription factor bound the promoters and regulated genes involved in sulfur metabolism. Additionally, CYS-3 directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulation of sulfur import is an important aspect of regulation by CYS-3. CYS-3 also directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism. IMPORTANCE Identification of nutrients present in the environment is a challenge common to all organisms. Sulfur is an important nutrient source found in proteins, lipids, and electron carriers that are required for the survival of filamentous fungi such as Neurospora crassa. Here, we transcriptionally profiled the response of N. crassa to characterize the global response to sulfur starvation. We also used DNA affinity purification sequencing to identify the direct downstream targets of the transcription factor responsible for regulating genes involved in sulfur uptake and assimilation. Along with genes involved in sulfur metabolism, this transcription factor regulated a number of uncharacterized transporter genes and genes involved in mitochondrial electron transfer. Our data also suggest a connection between sulfur, nitrogen, and carbon metabolism, indicating that the regulation of a number of metabolic pathways is intertwined.

Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species' cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward., (© 2021. The Author(s).)

Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors that activate genes necessary to utilize specific nitrogen sources in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1 , that is required for utilization of the nonpreferred nitrogen sources proline, branched-chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources, which require metabolic processing before being used as a nitrogen source, is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and the pathway-specific transcription factors NIT-4 and AMN-1 in directly regulating genes involved in nitrogen utilization. Although previous studies suggested promoter binding by both a pathway-specific transcription factor and NIT-2 may be necessary for activation of nitrogen-responsive genes, our data show that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization., Competing Interests: The authors declare no competing interest.

Filamentous fungi, such as Neurospora crassa , are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling of N. crassa on 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors in N. crassa and characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [ Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a tightly resolved time series, from plant emergence to postanthesis, resulting in a dataset of nearly 400 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We also identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the delayed senescence, characteristic of the stay-green phenotype. Finally, we discovered a large-scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants' roots.

Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Transcription factors (TFs) play a key role in regulating plant development and response to environmental stimuli. While most genes revert to single copy after whole genome duplication (WGD) event, transcription factors are retained at a significantly higher rate. Little is known about how TF duplicates have diverged in their expression and regulation, the answer to which may contribute to a better understanding of the elevated retention rate among TFs., Results: Here we assessed what features may explain differences in the retention of TF duplicates and other genes using Arabidopsis thaliana as a model. We integrated 34 expression, sequence, and conservation features to build a linear model for predicting the extent of duplicate retention following WGD events among TFs and 19 groups of genes with other functions. We found that TFs was the least well predicted, demonstrating the features of TFs are substantially deviated from duplicate genes in other function groups. Consistent with this, the evolution of TF expression patterns and cis-regulatory cites favors the partitioning of ancestral states among the resulting duplicates: one "ancestral" TF duplicate retains most ancestral expression and cis-regulatory sites, while the "non-ancestral" duplicate is enriched for novel regulatory sites. By modeling the retention of ancestral expression and cis-regulatory states in duplicate pairs using a system of differential equations, we found that TF duplicate pairs in a partitioned state are preferentially maintained., Conclusions: These TF duplicates with asymmetrically partitioned ancestral states are likely maintained because one copy retains ancestral functions while the other, at least in some cases, acquires novel cis-regulatory sites that may be important for novel, adaptive traits.

Grass biomass is comprised chiefly of secondary walls that surround fiber and xylem cells. A regulatory network of interacting transcription factors in part regulates cell wall thickening. We identified Brachypodium distachyon SECONDARY WALL ASSOCIATED MYB1 (SWAM1) as a potential regulator of secondary cell wall biosynthesis based on gene expression, phylogeny, and transgenic plant phenotypes. SWAM1 interacts with cellulose and lignin gene promoters with preferential binding to AC-rich sequence motifs commonly found in the promoters of cell wall-related genes. SWAM1 overexpression (SWAM-OE) lines had greater above-ground biomass with only a slight change in flowering time while SWAM1 dominant repressor (SWAM1-DR) plants were severely dwarfed with a striking reduction in lignin of sclerenchyma fibers and stem epidermal cell length. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. There was no reduction in bioconversion yield in SWAM1-OE lines; however, it was significantly increased for SWAM1-DR samples. Phylogenetic and syntenic analyses strongly suggest that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is not in the Brassicaceae. Collectively, these data suggest that SWAM1 is a transcriptional activator of secondary cell wall thickening and biomass accumulation in B. distachyon., (© 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.)

Maintenance of cell integrity and cell-to-cell communication are fundamental biological processes. Filamentous fungi, such as Neurospora crassa , depend on communication to locate compatible cells, coordinate cell fusion, and establish a robust hyphal network. Two MAP kinase (MAPK) pathways are essential for communication and cell fusion in N. crassa : the cell wall integrity/MAK-1 pathway and the MAK-2 (signal response) pathway. Previous studies have demonstrated several points of cross-talk between the MAK-1 and MAK-2 pathways, which is likely necessary for coordinating chemotropic growth toward an extracellular signal, and then mediating cell fusion. Canonical MAPK pathways begin with signal reception and end with a transcriptional response. Two transcription factors, ADV-1 and PP-1, are essential for communication and cell fusion. PP-1 is the conserved target of MAK-2, but it is unclear what targets ADV-1. We did RNA sequencing on Δ adv-1 , Δ pp-1 , and wild-type cells and found that ADV-1 and PP-1 have a shared regulon including many genes required for communication, cell fusion, growth, development, and stress response. We identified ADV-1 and PP-1 binding sites across the genome by adapting the in vitro method of DNA-affinity purification sequencing for N. crassa To elucidate the regulatory network, we misexpressed each transcription factor in each upstream MAPK deletion mutant. Misexpression of adv-1 was sufficient to fully suppress the phenotype of the Δ pp-1 mutant and partially suppress the phenotype of the Δ mak-1 mutant. Collectively, our data demonstrate that the MAK-1/ADV-1 and MAK-2/PP-1 pathways form a tight regulatory network that maintains cell integrity and mediates communication and cell fusion., (Copyright © 2018 by the Genetics Society of America.)

Among modern foraging societies, men hunt more than women, who mostly target relatively low-quality, reliable resources (i.e., plants). This difference has long been assumed to reflect human female reproductive constraints, particularly caring for and provisioning mates and offspring. Long-term studies of chimpanzees (Pan troglodytes) enable tests of hypotheses about the possible origins of human sex differences in hunting, prior to pair-bonding and regular provisioning. We studied two eastern chimpanzee communities (Kasekela, Mitumba) in Gombe, Tanzania and one (Kanyawara) in Kibale, Uganda. Relative to males, females had low hunting rates in all three communities, even where they encountered red colobus monkeys (the primary prey of chimpanzees) as often as males did. There was no evidence that clinging offspring hampered female hunting. Instead, consistent with the hypothesis that females should be more risk-averse than males, females at all three sites specialized in low-cost prey (terrestrial/sedentary prey at Gombe; black and white colobus monkeys at Kanyawara). Female dominance rank was positively correlated with red colobus hunting probability only at Kasekela, suggesting that those in good physical condition were less sensitive to the costs of possible failure. Finally, the potential for carcass appropriation by males deterred females at Kasekela (but not Kanyawara or Mitumba) from hunting in parties containing many adult males. Although chimpanzees are not direct analogs of the last common ancestor (LCA) of Pan and Homo, these results suggest that before the emergence of social obligations regarding sharing and provisioning, constraints on hunting by LCA females did not necessarily stem from maternal care. Instead, they suggest that a risk-averse foraging strategy and the potential for losing prey to males limited female predation on vertebrates. Sex differences in hunting behavior would likely have preceded the evolution of the sexual division of labor among modern humans., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro-expressed TF, and TF-DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be derived. A researcher with molecular biology experience should be able to follow this protocol, processing up to 400 samples per week.

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The plant hormone auxin is perceived by a family of F-box proteins called the TIR1/AFBs. Phylogenetic studies reveal that these proteins fall into four clades in flowering plants called TIR1, AFB2, AFB4, and AFB6. Genetic studies indicate that members of the TIR1 and AFB2 groups act as positive regulators of auxin signaling by promoting the degradation of the Aux/IAA transcriptional repressors. In this report, we demonstrate that both AFB4 and AFB5 also function as auxin receptors based on in vitro assays. We also provide genetic evidence that AFB4 and AFB5 are targets of the picloram family of auxinic herbicides in addition to indole-3-acetic acid. In contrast to previous studies we find that null afb4 alleles do not exhibit obvious defects in seedling morphology or auxin hypersensitivity. We conclude that AFB4 and AFB5 act in a similar fashion to other members of the family but exhibit a distinct auxin specificity., (Copyright © 2016 Prigge et al.)

An increase in faunivory is a consistent component of human evolutionary models. Animal matter is energy- and nutrient-dense and can provide macronutrients, minerals, and vitamins that are limited or absent in plant foods. For female humans and other omnivorous primates, faunivory may be of particular importance during the costly periods of pregnancy and early lactation. Yet, because animal prey is often monopolizable, access to fauna among group-living primates may be mediated by social factors such as rank. Wild chimpanzees (Pan troglodytes) across Africa habitually consume insects and/or vertebrates. However, no published studies have examined patterns of female chimpanzee faunivory during pregnancy and early lactation relative to non-reproductive periods, or by females of different rank. In this study, we assessed the influence of reproductive state and dominance rank on the consumption of fauna (meat and insects) by female chimpanzees of Gombe National Park, Tanzania. Using observational data collected over 38 years, we tested (a) whether faunivory varied by reproductive state, and (b) if high-ranking females spent more time consuming fauna than lower-ranking females. In single-factor models, pregnant females consumed more meat than lactating and baseline (meaning not pregnant and not in early lactation) females, and high-ranking females consumed more meat than lower-ranking females. A two-factor analysis of a subset of well-sampled females identified an interaction between rank and reproductive state: lower-ranking females consumed more meat during pregnancy than lower-ranking lactating and baseline females did. High-ranking females did not significantly differ in meat consumption between reproductive states. We found no relationships between rank or reproductive state with insectivory. We conclude that, unlike insectivory, meat consumption by female chimpanzees is mediated by both reproductive state and social rank. We outline possible mechanisms for these patterns, relate our findings to meat-eating patterns in women from well-studied hunter-gatherer societies, and discuss potential avenues for future research., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The T-DNA sequence-indexed mutant collections contain insertional mutants for most Arabidopsis thaliana genes and have played an important role in plant biology research for almost two decades. By providing a large source of mutant alleles for in vivo characterization of gene function, this resource has been leveraged thousands of times to study a wide range of problems in plant biology. Our primary goal in this chapter is to provide a general guide to strategies for the effective use of the data and materials in these collections. To do this, we provide a general introduction to the T-DNA insertional sequence-indexed mutant collections with a focus on how best to use the available data sources for good line selection. As isolation of a homozygous line is a common next step once a potential disruption line has been identified, the second half of the chapter provides a step-by-step guide for the design and implementation of a T-DNA genotyping pipeline. Finally, we describe interpretation of genotyping results and include a troubleshooting section for common types of segregation distortions that we have observed. In this chapter we introduce both basic concepts and specific applications to both new and more experienced users of the collections for the design and implementation of small- to large-scale genotyping pipelines.

Understanding the benefits and costs of acquiring and consuming different forms of animal matter by primates is critical for identifying the selective pressures responsible for increased meat consumption in the hominin lineage. Chimpanzees (Pan troglodytes) are unusual among primates in the amount of vertebrate prey they consume. Still, surprisingly little is known about the nutritional benefits of eating meat for this species. In order to understand why chimpanzees eat vertebrates, it is critical to consider the relative benefits and costs of other types of faunivory - including invertebrates. Although we lack specific nutritional data on the flesh and organs of chimpanzee prey, the macronutrient profiles of insects and wild vertebrate meat are generally comparable on a gram-to-gram basis. There are currently very few data on the micronutrient (vitamin and mineral) content of meat consumed by chimpanzees. With few exceptions, the advantages of hunting vertebrate prey include year-round availability, rapid acquisition of larger packages and reduced handling/processing time (once prey are encountered or detected). The disadvantages of hunting vertebrate prey include high potential acquisition costs per unit time (energy expenditure and risk of injury) and greater contest competition with conspecifics. Acquiring an equivalent mass of invertebrates (to match even a small scrap of meat) is possible, but typically takes more time. Furthermore, in contrast to vertebrate prey, some insect resources are effectively available only at certain times of the year. Here we identify the critical data needed to test our hypothesis that meat scraps may have a higher (or at least comparable) net benefit:cost ratio than insect prey. This would support the 'meat scrap' hypothesis as an explanation for why chimpanzees hunt in groups even when doing so does not maximize an individual's energetic gain., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Insectivory is hypothesized to be an important source of macronutrients, minerals, and vitamins for chimpanzees (Pan troglodytes), yet nutritional data based on actual intake are lacking. Drawing on observations from 2008 to 2010 and recently published nutritional assays, we determined the energy, macronutrient and mineral yields for termite-fishing (Macrotermes), ant-dipping (Dorylus), and ant-fishing (Camponotus) by the Kasekela chimpanzees of Gombe National Park, Tanzania. We also estimated the yields from consumption of weaver ants (Oecophylla) and termite alates (Macrotermes and Pseudacanthotermes). On days when chimpanzees were observed to prey on insects, the time spent in insectivorous behavior ranged from <1 min to over 4 h. After excluding partial bouts and those of <1 min duration, ant-dipping bouts were of significantly shorter duration than the other two forms of tool-assisted insectivory but provided the highest mass intake rate. Termite-fishing bouts were of significantly longer duration than ant-dipping and had a lower mass intake rate, but provided higher mean and maximum mass yields. Ant-fishing bouts were comparable to termite-fishing bouts in duration but had significantly lower mass intake rates. Mean and maximum all-day yields from termite-fishing and ant-dipping contributed to or met estimated recommended intake (ERI) values for a broad array of minerals. The mean and maximum all-day yields of other insects consistently contributed to the ERI only for manganese. All forms of insectivory provided small but probably non-trivial amounts of fat and protein. We conclude that different forms of insectivory have the potential to address different nutritional needs for Kasekela chimpanzees. Other than honeybees, insects have received little attention as potential foods for hominins. Our results suggest that ants and (on a seasonal basis) termites would have been viable sources of fat, high-quality protein and minerals for extinct hominins employing Pan-like subsistence technology in East African woodlands., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Humans, all great ape species, and some lesser apes consume insects. Insects can provide comparable nutritional yields to meat on a gram-for-gram basis and may serve as an important source of energy, fat, protein, minerals, and vitamins for hominoids. Although potential insect prey are abundant in ape habitats, patterns of insectivory are not consistent across species or populations. Efforts to understand these patterns are complicated by a lack of nutritional data. We collected samples of insects consumed by the Kasekela chimpanzee community of Gombe National Park, Tanzania, as well as of some insects found within the community range and ignored by these chimpanzees but known to be preyed upon by Pan elsewhere. We determined the gross energy (GE), estimated metabolizable energy (ME), fat, protein, fiber, and ash content of these samples following standard methodologies. We use these data to test the hypothesis that Kasekela chimpanzees choose insect prey (at least in part) based on energy and/or macronutrient content. On a fresh-weight, per-gram basis, the insect prey consumed by Kasekela chimpanzees had significantly higher fat and lower ash content than other assayed insects, and on a fresh-weight, per-foraging-unit ("per-insect," "per-dip," or "per-nest") basis were significantly higher in GE, fat, and protein. On a per-gram basis, the assayed insects were generally comparable in energy and macronutrients to wild vertebrate meat. We conclude that Kasekela chimpanzees do favor insects that are high in energy, fat, and protein, and that the potential macronutrient yields from some forms of insectivory are not trivial., (Copyright © 2012 Wiley Periodicals, Inc.)

Chimpanzees exhibit cultural variation, yet examples of successful cultural transmission between wild communities are lacking. Here we provide the first account of tool-assisted predation ("ant fishing") on Camponotus ants by the Kasekela and Mitumba communities of Gombe National Park. We then consider three hypotheses for the appearance and spread of this behavior in Kasekela: (1) changes in prey availability or other environmental factors, (2) innovation, and (3) introduction. Ant fishing was recognized as habitual in the Mitumba community by 1992, soon after their habituation began. Apart from one session in 1978, Camponotus predation (typically with tools) was documented in the Kasekela community beginning only in 1994, despite decades of prior observation. By February 2010, ant fishing was customary in Kasekela and with one exception was practiced exclusively by chimpanzees born after 1981 and immigrant females. We hypothesize that changes in insect prey availability over time and/or the characteristics of one popular ant-fishing site may have influenced the establishment of ant fishing. Though innovation cannot be completely ruled out, the circumstantial evidence suggests that a Mitumba immigrant introduced ant fishing to Kasekela. We submit that this report represents the first documented case of successful transmission of a novel cultural behavior between wild chimpanzee communities.

Chimpanzee responses to the death of a group member have rarely been observed in the wild and most instances involve infant deaths. One of the very few detailed accounts of a group's response to the death of an adult community member is from Gombe National Park, Tanzania, where Teleki [Folia Primatologica 20:81-94, 1973] observed the responses of 16 chimpanzees to an accidental death, none of whom touched the body. Now, almost 40 years later, we report on the behaviors of 16 (different) Gombe individuals to the recently dead body of an adult female community member. In stark contrast to Teleki's account, we observed individual chimpanzees' responses to range from curious observation and passive investigation (e.g. smelling and grooming) to the shaking, dragging, and frustrated beating of the body. Variation across demographic groups is described and may reflect individuals' past experience with death. The implications of our observations are discussed in the context of core morbidity traits shared between humans and chimpanzees., (© 2011 Wiley Periodicals, Inc.)

Genotype is the primary determinate of phenotype. During the past two decades, however, there has been an emergent recognition of the epigenotype, a separate layer of heredity distinct from the primary DNA sequence that can have profound effects on phenotype. The epigenotype is a collection of chemical modifications to the DNA and nucleosomes in conjunction with noncoding RNA transcripts, and together these epigenetic marks act as a potent and expansive regulatory system for controlling gene expression. In this review, we discuss our current understanding of variation in epigenotype in the model plant Arabidopsis and how allelic differences attributable to epigenetic changes, or epialleles, can affect phenotype. We discuss examples of epialleles that have been created in the laboratory and others that have been identified in natural populations, because these two models provide complementary information regarding the genetic pathways, mechanisms of transmission, and biological and evolutionary context for the role of the epigenotype in phenotypic variation.

Epigenetic information, which may affect an organism's phenotype, can be stored and stably inherited in the form of cytosine DNA methylation. Changes in DNA methylation can produce meiotically stable epialleles that affect transcription and morphology, but the rates of spontaneous gain or loss of DNA methylation are unknown. We examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants propagated by single-seed descent for 30 generations. We identified 114,287 CG single methylation polymorphisms and 2485 CG differentially methylated regions (DMRs), both of which show patterns of divergence compared with the ancestral state. Thus, transgenerational epigenetic variation in DNA methylation may generate new allelic states that alter transcription, providing a mechanism for phenotypic diversity in the absence of genetic mutation.

The large collections of Arabidopsis thaliana sequence-indexed T-DNA insertion mutants are among the most important resources to emerge from the sequencing of the genome. Several laboratories around the world have used the Arabidopsis reference genome sequence to map T-DNA flanking sequence tags (FST) for over 325,000 T-DNA insertion lines. Over the past decade, phenotypes identified with T-DNA-induced mutants have played a critical role in advancing both basic and applied plant research. These widely used mutants are an invaluable tool for direct interrogation of gene function. However, most lines are hemizygous for the insertion, necessitating a genotyping step to identify homozygous plants for the quantification of phenotypes. This situation has limited the application of these collections for genome-wide screens. Isolating multiple homozygous insert lines for every gene in the genome would make it possible to systematically test the phenotypic consequence of gene loss under a wide variety of conditions. One major obstacle to achieving this goal is that 12% of genes have no insertion and 8% are only represented by a single allele. Generation of additional mutations to achieve full genome coverage has been slow and expensive since each insertion is sequenced one at a time. Recent advances in high-throughput sequencing technology open up a potentially faster and cost-effective means to create new, very large insertion mutant populations for plants or animals. With the combination of new tools for genome-wide studies and emerging phenotyping platforms, these sequence-indexed mutant collections are poised to have a larger impact on our understanding of gene function.

Unlike nearly all other nonhuman primates, great apes build sleeping nests. In Bwindi Impenetrable National Park, Uganda, chimpanzees build nests nightly and also build day nests. We investigated patterns of nest tree use by Bwindi chimpanzees to understand ecological influences on nest tree selection. We analyzed data on 3,414 chimpanzee nests located from 2000 to 2004. Chimpanzees at Bwindi were selective in their use of nest trees. Of at least 163 tree species known to occur in Bwindi [Butynski, Ecological survey of the Impenetrable (Bwindi) Forest, Uganda, and recommendations for its conservation and management. Report to the Government of Uganda, 1984], chimpanzees utilized only 38 species for nesting. Of these, four tree species (Cassipourea sp., Chrysophyllum gorungosanum, Drypetes gerrardii, and Teclea nobilis) accounted for 72.1% of all nest trees. There was considerable variation in nesting frequencies among the top four species between and within years. However, these species were used significantly more often for nesting than other species in 70.9% (39 of 55) of the months of this study. A Spearman rank correlation found no significant relationship between tree abundance and tree species preference. Ninety-three percent of all nests were constructed in food tree species, although not necessarily at the same time the trees bore food items used by chimpanzees. The results indicate that nesting tree species preferences exist. Bwindi chimpanzees' choice of nesting tree species does not appear to be dependent on tree species density or use of the tree for food. We discuss possible reasons for the selectivity in nest trees by the Bwindi population.

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs) that control transcript expression through posttranscriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5'-3' exoribonuclease, and ABH1/CBP80, a subunit of the mRNA cap binding complex, results in Arabidopsis plants manifesting myriad developmental defects. We find that ABH1/CBP80 is necessary to obtain proper mature miRNA levels, which suggests this protein affects the miRNA-mediated RNA silencing pathway. Additionally, we show that XRN4/EIN5 affects the levels of a smRNA class that is processed from both sense and antisense strands of approximately 130 endogenous transcripts that apparently are converted to double-stranded RNA (dsRNA) and subsequently processed. We find that the parent transcripts of these smRNAs accumulate in an uncapped form upon loss of XRN4/EIN5, which suggests that uncapped endogenous transcripts can become smRNA biogenesis substrates. Overall, our results reveal unexpected connections between RNA metabolism and silencing pathways.

Deciphering the multiple layers of epigenetic regulation that control transcription is critical to understanding how plants develop and respond to their environment. Using sequencing-by-synthesis technology we directly sequenced the cytosine methylome (methylC-seq), transcriptome (mRNA-seq), and small RNA transcriptome (smRNA-seq) to generate highly integrated epigenome maps for wild-type Arabidopsis thaliana and mutants defective in DNA methyltransferase or demethylase activity. At single-base resolution we discovered extensive, previously undetected DNA methylation, identified the context and level of methylation at each site, and observed local sequence effects upon methylation state. Deep sequencing of smRNAs revealed a direct relationship between the location of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in regions of RNA-DNA homology. Finally, strand-specific mRNA-seq revealed altered transcript abundance of hundreds of genes, transposons, and unannotated intergenic transcripts upon modification of the DNA methylation state.

Agrobacterium transfer DNA (T-DNA) is an effective plant mutagen that has been used to create sequence-indexed T-DNA insertion lines in Arabidopsis thaliana as a tool to study gene function. Creating T-DNA insertion lines requires a dependable method for locating the site of insertion in the genome. In this protocol, we describe an adapter ligation-mediated PCR method that we have used to screen a mutant library and identify over 150,000 T-DNA insertional mutants; the method can also be applied to map individual mutants. The procedure consists of three steps: a restriction enzyme-mediated ligation of an adapter to the genomic DNA; a PCR amplification of the T-DNA/genomic DNA junction with primers specific to the adapter and T-DNA; and sequencing of the T-DNA/genomic junction to enable mapping to the reference genome. In most cases, the sequenced genomic region extends to the T-DNA border, enabling the exact location of the insert to be identified. The entire process takes 2 weeks to complete.

Ethylene influences a number of processes in Arabidopsis (Arabidopsis thaliana) through the action of five receptors. In this study, we used high-resolution, time-lapse imaging to examine the long-term effects of ethylene on growing, etiolated Arabidopsis seedlings. These measurements revealed that ethylene stimulates nutations of the hypocotyls with an average delay in onset of over 6 h. The nutation response was constitutive in ctr1-2 mutants maintained in air, whereas ein2-1 mutants failed to nutate when treated with ethylene. Ethylene-stimulated nutations were also eliminated in etr1-7 loss-of-function mutants. Transformation of the etr1-7 mutant with a wild-type genomic ETR1 transgene rescued the nutation phenotype, further supporting a requirement for ETR1. Loss-of-function mutations in the other receptor isoforms had no effect on ethylene-stimulated nutations. However, the double ers1-2 ers2-3 and triple etr2-3 ers2-3 ein4-4 loss-of-function mutants constitutively nutated in air. These results support a model where all the receptors are involved in ethylene-stimulated nutations, but the ETR1 receptor is required and has a contrasting role from the other receptor isoforms in this nutation phenotype. Naphthylphthalamic acid eliminated ethylene-stimulated nutations but had no effect on growth inhibition caused by ethylene, pointing to a role for auxin transport in the nutation phenotype.

The strength of the evidence for population-level handedness in the great apes is a topic of considerable debate, yet there have been few studies of handedness in orangutans. We conducted a study of manual lateralization in a captive group of eight orangutans (Pongo pygmaeus) ranking the degrees of manual preference according to a defined framework. We analyzed five behavioral patterns: eat (one- and two-handed), make/modify tool, oral tool-use, and manual tool-use. Although some individuals showed significant manual preferences for one or more tasks, at the group-level both one-handed and two-handed eating, oral tool-use, and make/modify tool were ranked at level 1 (unlateralized). Manual tool-use was ranked at level 2, with four subjects demonstrating significant hand preferences, but no group-level bias to the right or left. Four subjects also showed hand specialization to the right or left across several tasks. These results are consistent with most previous studies of manual preference in orangutans. The emergence of manual lateralization in orangutans may relate to more complex manipulative tasks. We hypothesize that more challenging manual tasks elicit stronger hand preferences.

Observed patterns of variability in the food-processing behavior of white-faced capuchins (Cebus capucinus) across populations may reflect foraging traditions. However, there has been relatively little attention given to intrapopulation variability in food processing among groups and age/sex classes, making recent cross-population comparisons difficult to interpret. In this paper, we provide data on patterns of object use in foraging that we observed at Santa Rosa National Park, Costa Rica, for comparison with published data from a neighboring research site, Palo Verde National Park. We also describe the techniques used to process two food items consumed by Cebus capucinus at Santa Rosa, and discuss the factors that may underlie observed variability. We conducted a 6-month study on two groups of capuchins in 2001, and collected data on general activity and feeding patterns, rates and forms of object use, and distinctive processing techniques employed for two specific foods (Sloanea terniflora and Luehea candida). Rates of object-use behavior at Santa Rosa were considerably higher than those reported for Palo Verde and showed significant variation between groups and age/sex classes, as did patterns of Sloanea and Luehea processing. Observed differences in feeding rates between groups may reflect food availability or relative profitability, whereas variation between age/sex classes seems to reflect differences in the physical capabilities, foraging strategies, and the relative experience of mature and immature animals. Further research is needed to identify how a social context may influence the acquisition of food-processing techniques in juveniles and the development of foraging traditions in social groups., ((c) 2005 Wiley-Liss, Inc.)

Interpopulation variability in patterns of food processing, similar to what is described as "traditional" or "cultural" variation in chimpanzees (Pan troglodytes) and orangutans (Pongo pygmaeus), was identified in white-faced capuchins (Cebus capucinus). However, recent comparisons of food processing in capuchins were conducted only at the population level, with relatively little attention given to variability among groups, age/sex classes, or individuals. This paper examines variability in the processing of specific food types within the context of various social networks (i.e., patterns of association, rank, and kinship) among free-ranging Cebus capucinus at Santa Rosa National Park in Costa Rica. We collected data on two groups of white-faced capuchins in 2001, identifying rates of "food interest" for each individual, as well as forms of processing for specific food types. Juveniles exhibited the most interest in the food-processing behavior of other group members, and food interest was directed most frequently toward adult females. We identified distinctive processing techniques for several food items (Luehea candida pods, Sloanea terniflora fruits, and caterpillars) that facilitated comparisons among individuals within groups. Food-processing techniques for Sloanea fruit and caterpillars appeared to vary independently of the social networks examined in this study. However, we found evidence that variation in Luehea candida processing is to some degree linked to both patterns of association and social rank. The potential influence of these variables on observed food processing patterns warrants further scrutiny., ((c) 2005 Wiley-Liss, Inc.)

Ethylene signaling in plants is mediated by a family of ethylene receptors related to bacterial two-component regulators. Expression in yeast of ethylene-binding domains from the five receptor isoforms from Arabidopsis thaliana and five-receptor isoforms from tomato confirmed that all members of the family are capable of high-affinity ethylene-binding activity. All receptor isoforms displayed a similar level of ethylene binding on a per unit protein basis, while members of both subfamily I and subfamily II from Arabidopsis showed similar slow-release kinetics for ethylene. Quantification of receptor-isoform mRNA levels in receptor-deficient Arabidopsis lines indicated a direct correlation between total message level and total ethylene-binding activity in planta. Increased expression of remaining receptor isoforms in receptor-deficient lines tended to compensate for missing receptors at the level of mRNA expression and ethylene-binding activity, but not at the level of receptor signaling, consistent with specialized roles for family members in receptor signal output.

Responses to the plant hormone ethylene are mediated by a family of five receptors in Arabidopsis that act in the absence of ethylene as negative regulators of response pathways. In this study, we examined the rapid kinetics of growth inhibition by ethylene and growth recovery after ethylene withdrawal in hypocotyls of etiolated seedlings of wild-type and ethylene receptor-deficient Arabidopsis lines. This analysis revealed that there are two phases to growth inhibition by ethylene in wild type: a rapid phase followed by a prolonged, slower phase. Full recovery of growth occurs approximately 90 min after ethylene removal. None of the receptor null mutations tested had a measurable effect on the two phases of growth inhibition. However, loss-of-function mutations in ETR1, ETR2, and EIN4 significantly prolonged the time for recovery of growth rate after ethylene was removed. Plants with an etr1-6;etr2-3;ein4-4 triple loss-of-function mutation took longer to recover than any of the single mutants, while the ers1;ers2 double mutant had no effect on recovery rate, suggesting that receiver domains play a role in recovery. Transformation of the ers1-2;etr1-7 double mutant with wild-type genomic ETR1 rescued the slow recovery phenotype, while a His kinase-inactivated ETR1 construct did not. To account for the rapid recovery from growth inhibition, a model in which clustered receptors act cooperatively is proposed.

Eight captive orangutans (Pongo pygmaeus) were given wooden blocks embedded with raisins and bamboo as raw material for tool making in a study of manual laterality. In about three quarters of the raisin extraction bouts, the orangutans held the tool in the lips or teeth rather than in their hands. Three adult males and 2 adult females showed extreme (> or =92%) preference for oral tool use, a subadult male and an adult female used oral tools about half the time, and 1 adult female preferred manual tool use. Most oral tool users made short tools (approx. 4-10 cm long) that were held in the lips and (probably) supported by the tongue. Preference for oral tool use does not correlate with body weight, age or sex, but it may be related to hand size or individual preference. This is the first report of customary oral tool use as the norm in captive orangutans; it resembles the behavioral patterns reported by van Schaik et al. and Fox et al. in nature., (Copyright 2000 S. Karger AG, Basel)

Parasitic strategies are widely distributed across the angiosperms and are estimated to have evolved at least eight different times. Within the obligate hemiparasitic and holoparasitic members, elaborate strategies for host selection have emerged. Here, we demonstrate that in the parasitic Scrophulariceae Striga asiatica, for which signal-mediated host detection is critical, expansin mRNA provides a reliable and accurate downstream molecular marker for the transition to the parasitic mode. Three different expansin genes, saExp1, saExp2, and saExp3, are regulated by xenognostic quinones. saExp3 appears to function as a seedling expansin, and its mRNA is depleted within minutes after induction of the host attachment organ. saExp1 and saExp2 share less homology with the known expansins, and their transcripts accumulate linearly over a critical induction period. The regulation of these genes suggests that the resources for developmental commitment must accumulate to a defined threshold before commitment to organogenesis is terminal. When the induction signal is removed prematurely, the accumulated message decays with a time constant that correlates with the time required for additional signal exposures to reinduce parasitic development. These results suggest that sophisticated controls exist for the accumulation of the necessary components for terminal commitment to the parasitic mode. Furthermore, building on the redox dependence of the inducing signal, they suggest a model akin to a "molecular capacitor" for clocking organogenesis in S. asiatica.

Parasitic strategies within the angiosperms generally succeed by tightly coupling developmental transitions with host recognition signals in a process referred to as xenognosis. Within the Scrophulariaceae, Striga asiatica is among the most studied and best understood parasitic member with respect to the processes of host recognition. Specific xenognosins regulate seed germination, the development of the host attachment organ, the haustorium, and several later stages of host-parasite integration. Here we discuss the signals regulating the development of the haustorium, the critical vegetative/parasitic transition in the life cycle of this obligate parasite. We provide evidence for the localized production of H(2)O(2) at the Striga root tip and suggest how this oxidant is used to exploit host peroxidases and cell wall pectins to generate a simple benzoquinone signal. This benzoquinone xenognosin proves to be both necessary and sufficient for haustorial induction in cultured seedlings. Furthermore, evidence is provided that benzoquinone binding to a redox active site completes a "redox circuit" to mediate signal perception. This redox reaction regulates the time-dependent expression of specific marker genes critical for the development of the mature host attachment organ. These studies extend the emerging series of events necessary for the molecular regulation of organogenesis within the parasitic plants and suggest novel signaling features and molecular mechanisms that may be common across higher plants.

Parasitic strategies are widely distributed in the plant kingdom and frequently involve coupling parasite organogenesis with cues from the host. In Striga asiatica, for example, the cues that initiate the development of the host attachment organ, the haustorium, originate in the host and trigger the transition from vegetative to parasitic mode in the root meristem. This system therefore offers a unique opportunity to study the signals and mechanisms that control plant cell morphogenesis. Here we establish that the biological activity of structural analogs of the natural inducer displays a marked dependence on redox potential and suggest the existence of a semiquinone intermediate. Building on chemistry that exploits the energetics of such an intermediate, cyclopropyl-p-benzoquinone (CPBQ) is shown to be a specific inhibitor of haustorial development. These data are consistent with a model where haustorial development is initiated by the completion of a redox circuit.