Contracting eastern African C4 grasslands during the extinction of Paranthropus boisei.

The extinction of the Paranthropus boisei estimated to just before 1 Ma occurred when C4 grasslands dominated landscapes of the Eastern African Rift System (EARS). P. boisei has been characterized as an herbivorous C4 specialist, and paradoxically, its demise coincided with habitats favorable to its dietary ecology. Here we report new pedogenic carbonate stable carbon (δ13CPC) and oxygen (δ18OPC) values (nodules = 53, analyses = 95) from an under-sampled interval (1.4-0.7 Ma) in the Turkana Basin (Kenya), one of the most fossiliferous locales of P. boisei. We combined our new results with published δ13CPC values from the EARS dated to 3-0 Ma, conducted time-series analysis of woody cover (ƒWC), and compared the EARS ƒWC trends to regional and global paleo-environmental and -climatic datasets. Our results demonstrate that the long-term rise of C4 grasslands was punctuated by a transient but significant increase in C3 vegetation and warmer temperatures, coincident with the Mid-Pleistocene Transition (1.3-0.7 Ma) and implicating a short-term rise in pCO2. The contraction of C4 grasslands escalated dietary competition amongst the abundant C4-feeders, likely influencing P. boisei's demise.

Hematite reconstruction of Late Triassic hydroclimate over the Colorado Plateau.

Hematite is the most abundant surficial iron oxide on Earth resulting from near-surface processes that make it important for addressing numerous geologic problems. While red beds have proved to be excellent paleomagnetic recorders, the early diagenetic origin of hematite in these units is often questioned. Here, we validate pigmentary hematite ("pigmentite") as a proxy indicator for the Late Triassic environment and its penecontemporaneous origin by analyzing spectrophotometric measurements of a 14.5-My-long red bed sequence in scientific drill core CPCP-PFNP13-1A of the Chinle Formation, Arizona. Pigmentite concentrations in the red beds track the evolving pattern of the Late Triassic monsoon and indicate a long-term rise in aridity beginning at ∼215 Ma followed by increased oscillatory climate change at ∼213 Ma. These monsoonal changes are attributed to the northward drift of the Colorado Plateau as part of Laurentia into the arid subtropics during a time of fluctuating CO2 Our results refine the record of the Late Triassic monsoon and indicate significant changes in rainfall proximal to the Adamanian-Revueltian biotic transition that thus may have contributed to apparent faunal and floral events at 216 to 213 Ma.

Revisiting the pedogenic carbonate isotopes and paleoenvironmental interpretation of Kanapoi.

Reconstructed habitats of Australopithecus anamensis at Kanapoi by Wynn (2000) yielded evidence for both wooded and grassy environments. Wynn's study was based on stable isotopic (δ13CPC, δ18OPC) analyses of a small sample of pedogenic nodules (n = 14) collected from paleosols spanning Kanapoi's stratigraphic interval. Whether this small sample size adequately characterized Kanapoi's vegetation or was the result of time averaging remains unclear. To address this uncertainty, we sampled Kanapoi paleosols at 39 locations (78 analyses) from laterally extensive units. Our data demonstrate that Kanapoi offered A. anamensis diverse habitats distributed in temporally discrete stratigraphic horizons. Habitat heterogeneity appears to have been a real aspect of Kanapoi paleoenvironments and not an artifact of Wynn's (2000) small sample size or time averaging. We suggest habitat heterogeneity was influenced by the location of Kanapoi at the confluence of fluvial, deltaic, and lacustrine depositional environments. We also compared Kanapoi's δ13CPC and δ18OPC values to those of other Pliocene hominin localities in eastern Africa dated to 4.5-3.7 Ma. Kanapoi's δ18OPC values are significantly higher than most sites, potentially reflecting regional variability in water source δ18O values and/or more arid climatic conditions. Kanapoi's δ13CPC values indicate significantly more woody cover than at all other sites except those in the Turkana Basin. Kanapoi provided A. anamensis with a wide range of C3-C4 resources as the C4 biome spread across eastern Africa. [Wynn, J.G., 2000. Paleosols, stable carbon isotopes and paleoenvironmental interpretation of Kanapoi, Northern Kenya. J. Hum. Evol. 39, 411-432.].

Empirical evidence for stability of the 405-kiloyear Jupiter-Venus eccentricity cycle over hundreds of millions of years.

The Newark-Hartford astrochronostratigraphic polarity timescale (APTS) was developed using a theoretically constant 405-kiloyear eccentricity cycle linked to gravitational interactions with Jupiter-Venus as a tuning target and provides a major timing calibration for about 30 million years of Late Triassic and earliest Jurassic time. While the 405-ky cycle is both unimodal and the most metronomic of the major orbital cycles thought to pace Earth's climate in numerical solutions, there has been little empirical confirmation of that behavior, especially back before the limits of orbital solutions at about 50 million years before present. Moreover, the APTS is anchored only at its younger end by U-Pb zircon dates at 201.6 million years before present and could even be missing a number of 405-ky cycles. To test the validity of the dangling APTS and orbital periodicities, we recovered a diagnostic magnetic polarity sequence in the volcaniclastic-bearing Chinle Formation in a scientific drill core from Petrified Forest National Park (Arizona) that provides an unambiguous correlation to the APTS. New high precision U-Pb detrital zircon dates from the core are indistinguishable from ages predicted by the APTS back to 215 million years before present. The agreement shows that the APTS is continuous and supports a stable 405-kiloyear cycle well beyond theoretical solutions. The validated Newark-Hartford APTS can be used as a robust framework to help differentiate provinciality from global temporal patterns in the ecological rise of early dinosaurs in the Late Triassic, amongst other problems.

Fragment-Based Discovery of Dual JC Virus and BK Virus Helicase Inhibitors.

There are currently no treatments for life-threatening infections caused by human polyomaviruses JCV and BKV. We therefore report herein the first crystal structure of the hexameric helicase of JCV large T antigen (apo) and its use to drive the structure-based design of dual JCV and BKV ATP-competitive inhibitors. The crystal structures obtained by soaking our early inhibitors into the JCV helicase allowed us to rapidly improve the biochemical activity of our inhibitors from 18 µM for the early 6-(2-methoxyphenyl)- and the 6-(2-ethoxyphenyl)-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole hits 1a and 1b to 0.6 µM for triazolopyridine 12i. In addition, we were able to demonstrate measurable antiviral activity in Vero cells for our thiazolopyridine series in the absence of marked cytotoxicity, thus confirming the usefulness of this approach.

Enhanced and stabilized arsenic retention in microcosms through the microbial oxidation of ferrous iron by nitrate.

Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. Here, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated by the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6-7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. These results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers.

Chronostratigraphy of KNM-ER 3733 and other Area 104 hominins from Koobi Fora.

A magnetostratigraphy for ∼ 60 m of Koobi Fora Formation sediment in Area 104 was derived from 46 oriented samples that produced well-resolved characteristic magnetizations from progressive thermal demagnetization. Approximately 59 m below the Morte Tuff, previously dated to ∼ 1.51 Ma (millions of years ago), the Olduvai-Matuyama boundary (∼ 1.78 Ma) was found to be at the level of marker bed A2--inconsistent with the Area 102 type section and thus contrary to fossil dating schemes that utilize temporal equivalence between A2 [104] and A2 [102]. The magnetostratigraphic data, coupled with the Morte Tuff, provide a means to interpolate new ages for marker beds A2 [104] and the White Tuff, as well as multiple Area 104 hominin fossils. Noteworthy is the new date of ∼ 1.63 Ma for KNM-ER 3733, which now implicates KNM-ER 2598 as the sole early African Homo erectus fossil demonstrably older than Dmanisi and Java Homo specimens. Re-dating KNM-ER 3733 creates a ∼ 300-kyr gap at 1.9 to 1.6 Ma in the African fossil record of H. erectus, which might be partially spanned by hand axes recently dated at ∼ 1.76 Ma, if the Acheulian is indeed proprietary to this species.

3.3-million-year-old stone tools from Lomekwi 3, West Turkana, Kenya.

Human evolutionary scholars have long supposed that the earliest stone tools were made by the genus Homo and that this technological development was directly linked to climate change and the spread of savannah grasslands. New fieldwork in West Turkana, Kenya, has identified evidence of much earlier hominin technological behaviour. We report the discovery of Lomekwi 3, a 3.3-million-year-old archaeological site where in situ stone artefacts occur in spatiotemporal association with Pliocene hominin fossils in a wooded palaeoenvironment. The Lomekwi 3 knappers, with a developing understanding of stone's fracture properties, combined core reduction with battering activities. Given the implications of the Lomekwi 3 assemblage for models aiming to converge environmental change, hominin evolution and technological origins, we propose for it the name 'Lomekwian', which predates the Oldowan by 700,000 years and marks a new beginning to the known archaeological record.

Pedogenic carbonate stable isotopic evidence for wooded habitat preference of early Pleistocene tool makers in the Turkana Basin.

The origin and evolution of early Pleistocene hominin lithic technologies in Africa occurred within the context of savanna grassland ecosystems. The Nachukui Formation of the Turkana Basin in northern Kenya, containing Oldowan and Acheulean tool assemblages and fossil evidence for early members of Homo and Paranthropus, provides an extensive spatial and temporal paleosol record of early Pleistocene savanna flora. Here we present new carbon isotopic (δ(13)CVPDB) values of pedogenic carbonates (68 nodules, 193 analyses) from the Nachukui Formation in order to characterize past vegetation structure and change through time. We compared three members (Kalochoro, Kaitio, and Natoo) at five locations spanning 2.4-1.4Ma and sampled in proximity to hominin archaeological and paleontological sites. Our results indicate diverse habitats showing a mosaic pattern of vegetation cover at each location yet demonstrate grassland expansion through time influenced by paleogeography. Kalochoro floodplains occurred adjacent to large river systems, and paleosols show evidence of C3 woodlands averaging 46-50% woody cover. Kaitio habitats were located along smaller rivers and lake margins. Paleosols yielded evidence for reduced portions of woody vegetation averaging 34-37% woody cover. Natoo environments had the highest percentage of grasslands averaging 21% woody cover near a diminishing Lake Turkana precursor. We also compared paleosol δ(13)CVPDB values of lithic archaeological sites with paleosol δ(13)CVPDB values of all environments available to hominins at 2.4-1.4Ma in the Nachukui and Koobi Fora Formations. Grassy environments became more widespread during this interval; woody canopy cover mean percentages steadily decreased by 12%. However, significantly more wooded savanna habitats were present in the vicinity of lithic archaeological sites and did not mirror the basin-wide trend of grassland spread. Hominin lithic archaeological sites consistently demonstrated woody cover circa 40% throughout our study interval and were 4-12% more woody than coeval basin environs. We propose that Turkana Basin early tool makers may have preferred a more wooded portion of the savanna ecosystem to reduce heat stress and to gain differential access to potable water, raw materials, animal carcasses, and edible plants.

An earlier origin for the Acheulian.

The Acheulian is one of the first defined prehistoric techno-complexes and is characterized by shaped bifacial stone tools. It probably originated in Africa, spreading to Europe and Asia perhaps as early as ∼1 million years (Myr) ago. The origin of the Acheulian is thought to have closely coincided with major changes in human brain evolution, allowing for further technological developments. Nonetheless, the emergence of the Acheulian remains unclear because well-dated sites older than 1.4 Myr ago are scarce. Here we report on the lithic assemblage and geological context for the Kokiselei 4 archaeological site from the Nachukui formation (West Turkana, Kenya) that bears characteristic early Acheulian tools and pushes the first appearance datum for this stone-age technology back to 1.76 Myr ago. Moreover, co-occurrence of Oldowan and Acheulian artefacts at the Kokiselei site complex indicates that the two technologies are not mutually exclusive time-successive components of an evolving cultural lineage, and suggests that the Acheulian was either imported from another location yet to be identified or originated from Oldowan hominins at this vicinity. In either case, the Acheulian did not accompany the first human dispersal from Africa despite being available at the time. This may indicate that multiple groups of hominins distinguished by separate stone-tool-making behaviours and dispersal strategies coexisted in Africa at 1.76 Myr ago.

The age of the 20 meter Solo River terrace, Java, Indonesia and the survival of Homo erectus in Asia.

Homo erectus was the first human lineage to disperse widely throughout the Old World, the only hominin in Asia through much of the Pleistocene, and was likely ancestral to H. sapiens. The demise of this taxon remains obscure because of uncertainties regarding the geological age of its youngest populations. In 1996, some of us co-published electron spin resonance (ESR) and uranium series (U-series) results indicating an age as young as 35-50 ka for the late H. erectus sites of Ngandong and Sambungmacan and the faunal site of Jigar (Indonesia). If correct, these ages favor an African origin for recent humans who would overlap with H. erectus in time and space. Here, we report (40)Ar/(39)Ar incremental heating analyses and new ESR/U-series age estimates from the "20 m terrace" at Ngandong and Jigar. Both data sets are internally consistent and provide no evidence for reworking, yet they are inconsistent with one another. The (40)Ar/(39)Ar analyses give an average age of 546±12 ka (sd±5 se) for both sites, the first reliable radiometric indications of a middle Pleistocene component for the terrace. Given the technical accuracy and consistency of the analyses, the argon ages represent either the actual age or the maximum age for the terrace and are significantly older than previous estimates. Most of the ESR/U-series results are older as well, but the oldest that meets all modeling criteria is 143 ka+20/-17. Most samples indicated leaching of uranium and likely represent either the actual or the minimum age of the terrace. Given known sources of error, the U-series results could be consistent with a middle Pleistocene age. However, the ESR and (40)Ar/(39)Ar ages preclude one another. Regardless, the age of the sites and hominins is at least bracketed between these estimates and is older than currently accepted.

Practical aspects of NMR-based fragment screening.

NMR spectroscopy is a popular and highly versatile screening method for fragment-based drug discovery. NMR methods are capable of robustly detecting the binding of fragments to macromolecular targets over an extraordinarily broad affinity range (from covalent to millimolar). This chapter provides a stepwise process for creating an NMR-based fragment screening program. The construction of fragment libraries is described, including compound selection, plating of stocks, and preparation of mixtures. Guidance is given for designing fragment screens, such as choosing the appropriate NMR screening format and method, and optimizing the sample conditions and experimental parameters. The identification and validation of screening hits is described, and a number of potential pitfalls are discussed. Rather than detailing one specific screening protocol, this chapter outlines the available options and provides information to enable users to design their own customized fragment screening programs.

Crystal structure of the ectodomain complex of the CGRP receptor, a class-B GPCR, reveals the site of drug antagonism.

Dysregulation of the calcitonin gene-related peptide (CGRP), a potent vasodilator, is directly implicated in the pathogenesis of migraine. CGRP binds to and signals through the CGRP receptor (CGRP-R), a heterodimer containing the calcitonin receptor-like receptor (CLR), a class B GPCR, and RAMP1, a receptor activity-modifying protein. We have solved the crystal structure of the CLR/RAMP1 N-terminal ectodomain heterodimer, revealing how RAMPs bind to and potentially modulate the activities of the CLR GPCR subfamily. We also report the structures of CLR/RAMP1 in complex with the clinical receptor antagonists olcegepant (BIBN4096BS) and telcagepant (MK0974). Both drugs act by blocking access to the peptide-binding cleft at the interface of CLR and RAMP1. These structures illustrate, for the first time, how small molecules bind to and modulate the activity of a class B GPCR, and highlight the challenges of designing potent receptor antagonists for the treatment of migraine and other class B GPCR-related diseases.

Refolding and characterization of a soluble ectodomain complex of the calcitonin gene-related peptide receptor.

The calcitonin gene-related peptide (CGRP) receptor is a heterodimer of two membrane proteins: calcitonin receptor-like receptor (CLR) and receptor activity-modifying protein 1 (RAMP1). CLR is a class B G-protein-coupled receptor (GPCR), possessing a characteristic large amino-terminal extracellular domain (ECD) important for ligand recognition and binding. Dimerization of CLR with RAMP1 provides specificity for CGRP versus related agonists. Here we report the expression, purification, and refolding of a soluble form of the CGRP receptor comprising a heterodimer of the CLR and RAMP1 ECDs. The extracellular protein domains corresponding to residues 23-133 of CLR and residues 26-117 of RAMP1 were shown to be sufficient for formation of a stable, monodisperse complex. The binding affinity of the purified ECD complex for the CGRP peptide was significantly lower than that of the native receptor (IC(50) of 12 microM for the purified ECD complex vs 233 pM for membrane-bound CGRP receptor), indicating that other regions of CLR and/or RAMP1 are important for peptide agonist binding. However, high-affinity binding to known potent and specific nonpeptide antagonists of the CGRP receptor, including olcegepant and telcagepant (K(D) < 0.02 muM), as well as N-terminally truncated peptides and peptide analogues (140 nM to 1.62 microM) was observed.

Stratigraphy, correlation, and age estimates for fossils from Area 123, Koobi Fora.

Geological data from the Bura Hasuma region at Koobi Fora provide important constraints for estimating the ages of hominin fossils recovered there, including the cranium KNM-ER 1813. Strata of the upper Burgi, KBS, and Okote members in this part of Koobi Fora reflect three depositional regimes driven by changing paleogeography through time. The upper Burgi and lowermost KBS sequence in the southern Bura Hasuma region accumulated in a lacustrine to delta front setting, with highly localized depositional patterns, limiting the lateral extent of lithostratigraphic markers. Farther north, uppermost upper Burgi through KBS member strata document a fluctuating lake margin, with complex facies patterns. This interval is marked by laterally extensive lithostratigraphic markers, including molluscan packstones, beach sandstones, and stromatolite beds. The uppermost KBS and Okote members show a transition to dominantly fluvial character, with localized and discontinuous accumulation. An age model for the richly fossiliferous Area 123 sequence demonstrates the complexity of terrestrial accumulation patterns. Early lacustrine and delta front accumulation is marked by fairly continuous sedimentation, and high accumulation rates (up to ca. 91 cm/k.yr.). The fluctuating lake margin interval reflects lower sedimentation rates coupled with intervals of exposure, decreasing accumulation significantly (to ca. 13 cm/k.yr.). The capping fluvial interval is marked by significant erosion surfaces, breaks which may drop the overall accumulation rate even lower (ca. 0.3 cm/k.yr.). The data provided here establish a geological framework at odds with a recent proposal of ages considerably younger (by ca. 250 k.yr.) for many of the fossils from Area 123 and elsewhere. Tests of age models demonstrate that the younger ages are not possible. While minor refinements to age estimates for fossils are indicated by improved chronostratigraphic control, in the case of KNM-ER 1813, an age of younger than 1.78 Ma is precluded on magnetostratigraphic grounds.

Plio-Pleistocene facies environments from the KBS Member, Koobi Fora Formation: implications for climate controls on the development of lake-margin hominin habitats in the northeast Turkana Basin (northwest Kenya).

Climate change is hypothesized as a cause of major events of Plio-Pleistocene East African hominin evolution, but the vertically discontinuous and laterally confined nature of the relevant geological records has led to difficulties with assessing probable links between the two. High-resolution sedimentary sequences from lacustrine settings can provide comprehensive data of environmental changes and detailed correlations with well-established orbital and marine records of climate. Hominin-bearing deposits from Koobi Fora Ridge localities in the northeast Turkana Basin of Kenya are an archive of Plio-Pleistocene lake-margin sedimentation though significant developmental junctures of northern African climates, East African environments, and hominin evolution. This study examines alluvial channel and floodplain, nearshore lacustrine, and offshore lacustrine facies environments for the approximately 136-m-thick KBS Member (Koobi Fora Formation) exposed at the Koobi Fora Ridge. Aspects of the facies environments record information on the changing hydrosedimentary dynamics of the lake margin and give insights into potential climatic controls. Seasonal/yearly climate changes are represented by the varve-like laminations in offshore mudstones and the slickensides, dish-shaped fractures, and other paleosol features overprinted on floodplain strata. Vertical shifts between facies environments, however, are interpreted to indicate lake-level fluctuations deriving from longer-term, dry-wet periods in monsoonal rainfall. Recurrence periods for the inferred lake-level changes range from about 10,000 to 50,000 years, and several are consistent with the average estimated timescales of orbital precession ( approximately 20,000 years) and obliquity ( approximately 40,000 years). KBS Member facies environments from the Koobi Fora Ridge document the development of lake-margin hominin habitats in the northeast Turkana Basin. Environmental changes in these habitats may be a result of monsoonal rainfall variations that derive from orbital insolation and/or glacial forcing.

Paleogeographic variations of pedogenic carbonate delta13C values from Koobi Fora, Kenya: implications for floral compositions of Plio-Pleistocene hominin environments.

Plio-Pleistocene East African grassland expansion and faunal macroevolution, including that of our own lineage, are attributed to global climate change. To further understand environmental factors of early hominin evolution, we reconstruct the paleogeographic distribution of vegetation (C(3)-C(4) pathways) by stable carbon isotope (delta(13)C) analysis of pedogenic carbonates from the Plio-Pleistocene Koobi Fora region, northeast Lake Turkana Basin, Kenya. We analyzed 202 nodules (530 measurements) from ten paleontological/archaeological collecting areas spanning environments over a 50-km(2) area. We compared results across subregions in evolving fluviolacustrine depositional environments in the Koobi Fora Formation from 2.0-1.5 Ma, a stratigraphic interval that temporally brackets grassland ascendancy in East Africa. Significant differences in delta(13)C values between subregions are explained by paleogeographic controls on floral composition and distribution. Our results indicate grassland expansion between 2.0 and 1.75 Ma, coincident with major shifts in basin-wide sedimentation and hydrology. Hypotheses may be correct in linking Plio-Pleistocene hominin evolution to environmental changes from global climate; however, based on our results, we interpret complexity from proximate forces that mitigated basin evolution. An approximately 2.5 Ma tectonic event in southern Ethiopia and northern Kenya exerted strong effects on paleography in the Turkana Basin from 2.0-1.5 Ma, contributing to the shift from a closed, lacustrine basin to one dominated by open, fluvial conditions. We propose basin transformation decreased residence time for Omo River water and expanded subaerial floodplain landscapes, ultimately leading to reduced proportions of wooded floras and the establishment of habitats suitable for grassland communities.

Crystal structure of the p38 alpha-MAPKAP kinase 2 heterodimer.

The p38 signaling pathway is activated in response to cell stress and induces production of proinflammatory cytokines. P38alpha is phosphorylated and activated in response to cell stress by MKK3 and MKK6 and in turn phosphorylates a number of substrates, including MAPKAP kinase 2 (MK2). We have determined the crystal structure of the unphosphorylated p38alpha-MK2 heterodimer. The C-terminal regulatory domain of MK2 binds in the docking groove of p38alpha, and the ATP-binding sites of both kinases are at the heterodimer interface. The conformation suggests an extra mechanism in addition to the regulation of the p38alpha and MK2 phosphorylation states that prevents phosphorylation of substrates in the absence of cell stress. Addition of constitutively active MKK6-DD results in rapid phosphorylation of the p38alpha-MK2 heterodimer.

Fragment-based drug discovery using the SHAPES method.

The SHAPES method is one of several fragment-based drug discovery methods developed in the last decade. Molecules containing drug-like fragments are screened using NMR methods to find weakly binding (0.1 µM to multi-mM) hits that are then transformed into potent, viable leads. This review analyzes ten years of SHAPES screens, in which potent leads were found for 70 - 80% of the targets screened, and discusses lessons learned about how best to apply fragment-based lead discovery in the pharmaceutical environment. Detailed examples of lead discovery and optimization for the kinases REDK and MK2 are given. Finally, future directions are considered and a strategy is proposed for increasing efficiency by coupling fragment-based screening with receptor-assisted inhibitor design (NMR-RAID).