Publication date: Available online 6 July 2018
Source: Journal of Genetics and Genomics
Author(s): Qi Zhao, Yu Sun, Dawei Wang, Hongwan Zhang, Kai Yu, Jian Zheng, Zhixiang Zuo
Publication date: Available online 5 July 2018
Source: International Journal of Psychophysiology
Author(s): Julie M. Schneider, Mandy J. Maguire
Event related potentials (ERPs) and time frequency analysis of the EEG can identify the temporally distinct coordination of groups of neurons across brain regions during sentence processing. Although there are strong arguments that ERP components and neural oscillations are driven by the same changes in the neural signal, others argue that the lack of clear associations between the two suggests oscillatory dynamics are more than just time frequency representations of ERP components, making it unclear how the two are related. The current study seeks to examine the neural activity underlying auditory sentence processing of both semantic and syntactic errors to clarify if ERP and time frequency analyses identify the same or unique neural responses. Thirty-nine adults completed an auditory semantic judgment task and a grammaticality judgment task. As expected, the semantic judgment task elicited a larger N400 and greater increase in theta power for semantic errors compared to correct sentences and the syntactic judgment task elicited a greater P600 and beta power decrease for both grammatical error types compared to syntactically correct sentences. Importantly, we identified a significant relationship between the N400 and P600 ERPs and theta and beta oscillatory dynamics during semantic and syntactic processing. These findings suggest that ERPs and neural oscillations measure similar neural processes; however, unaccounted for variance may indicate that neural oscillations provide additional information regarding fluctuations in power within a given frequency band. Future studies that vary semantic and syntactic complexity are necessary to understand the cognitive processes that are indexed by these oscillations.
Lumbar disc surgery for radicular leg pain is one of the most frequently performed spine procedures. In approximately 20% of patients poor outcome is achieved. The most complex cases have persistent leg pain without residual nerve root compression. Treatment for refractory cases is limited to medical pain management, spinal cord stimulation (SCS) and dorsal root ganglion stimulation (DRGS). For the latter two, fair to good results are obtained in only 50% of patients and costs and complication rates are high.
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This study assessed the utility of ultrasound-guided lateral transversus abdominis plane (TAP) block combined with rectus sheath (RS) block for peritoneal dialysis catheter placement surgery. Thirty consecutive patients with end-stage renal disease scheduled to have peritoneal dialysis catheter placement received a left lateral TAP block combined with RS block performed under ultrasound guidance. The TAP and RS blocks were, respectively, conducted with 15 ml of 0.5% ropivacaine and 10 ml of 0.5% ropivacaine. Pain intensity was evaluated by verbal rating scale during operation, and the degree of patient and surgeon satisfaction was qualified by a categorical scale. Twenty-nine patients received successful blocks without any other adjuvant anesthetic drugs. One patient required rescue analgesia with lidocaine infiltration. No complications related to regional anesthesia were noted. Ultrasound-guided left lateral TAP block combined with RS block can serve as the primary anesthetic modality for peritoneal dialysis catheter placement surgery.
Publication date: Available online 27 June 2018
Source: Anesthesiology Clinics
Author(s): Edward R. Mariano, Nabil M. Elkassabany
Publication date: Available online 15 June 2018
Source: Anesthesiology Clinics
Author(s): Lee A. Fleisher
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): John-Paul J. Pozek, Martin De Ruyter, Talal W. Khan
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Talal W. Khan, Smith Manion
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Neil N. Shah, Thomas R. Vetter
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Stanley W. Stead, Sharon K. Merrick
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Joseph W. Szokol, Keith J. Chamberlin
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Monaliza Gaw, Frank Rosinia, Thomas Diller
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): DeLaine Schmitz, Matthew T. Popovich
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Avery Tung
Objectives The first 6 weeks postpartum represent a time of significant adjustment and learning for parents. Healthcare providers accurately understanding parents' needs and preferences regarding support, education, and services during this critical time is essential for optimizing maternal and infant health. The first objective of this study was to explore parents' experiences adjusting to the parenting role during the first 6 weeks postpartum. The second objective was to elicit from parents where and how they sought support and information during the early postpartum period, and what hindered this process. Methods Five focus groups were conducted with 33 mothers and fathers of young children, stratified by ethnicity, education, and income. An interdisciplinary team thematically coded verbatim transcripts and identified emergent themes. Results Main themes included low confidence in parenting and sifting through parenting information. Additional themes included communicating with partner about changing roles, breastfeeding, maternal mental health, and maternal postpartum recovery. Low parenting confidence was closely linked with information seeking, yet participants expressed being overwhelmed by the task of managing conflicting parenting information. Women reported that providers focused on infant needs, leaving them feeling unprepared for their own mental and physical health needs. Conclusions for Practice Parents report extensive needs for education and support in the early postpartum period, yet also report feeling overwhelmed by the quantity of parenting information available. These findings suggest parents need and desire reliable healthcare education after discharge that includes parent health and adjustment.
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): John Allyn, Craig Curry
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Amanda J. Morris, Joseph A. Sanford, Edward J. Damrose, Samuel H. Wald, Bassam Kadry, Alex Macario
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Mark E. Hudson, Evan E. Lebovitz
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s): Amr E. Abouleish, Stanley W. Stead
Publication date: June 2018
Source: Anesthesiology Clinics, Volume 36, Issue 2
Author(s):
Publication date: Available online 30 June 2018
Source: Journal of Human Evolution
Author(s): Neil T. Roach, Andrew Du, Kevin G. Hatala, Kelly R. Ostrofsky, Jonathan S. Reeves, David R. Braun, John W.K. Harris, Anna K. Behrensmeyer, Brian G. Richmond
The ecological and selective forces that sparked the emergence of Homo's adaptive strategy remain poorly understood. New fossil and archaeological finds call into question previous interpretations of the grade shift that drove our ancestors' evolutionary split from the australopiths. Furthermore, issues of taphonomy and scale have limited reconstructions of the hominin habitats and faunal communities that define the environmental context of these behavioral changes. The multiple ∼1.5 Ma track surfaces from the Okote Member of the Koobi Fora Formation at East Turkana provide unique windows for examining hominin interactions with the paleoenvironment and associated faunas at high spatiotemporal resolution. These surfaces preserve the tracks of many animals, including cf. Homo erectus. Here, we examine the structure of the animal community that inhabited this landscape, considering effects of preservation bias by comparing the composition of the track assemblage to a skeletal assemblage from the same time and place. We find that the track and skeletal assemblages are similar in their representation of the vertebrate paleocommunity, with comparable levels of taxonomic richness and diversity. Evenness (equitability of the number of individuals per taxon) differs between the two assemblages due to the very different circumstances of body fossil versus track preservation. Both samples represent diverse groups of taxa including numerous water-dependent species, consistent with geological interpretations of the track site environments. Comparisons of these assemblages also show a pattern of non-random hominin association with a marginal lacustrine habitat relative to other vertebrates in the track assemblage. This evidence is consistent with behavior that included access to aquatic foods and possibly hunting by H. erectus in lake margins/edaphic grasslands. Such behaviors may signal the emergence of the adaptative strategies that define our genus.
Publication date: Available online 25 June 2018
Source: Journal of Human Evolution
Author(s): Christopher C. Gilbert, Stephen R. Frost, Kelsey D. Pugh, Monya Anderson, Eric Delson
Baboons (Papio hamadryas) are among the most successful extant primates, with a minimum of six distinctive forms throughout Sub-Saharan Africa. However, their presence in the fossil record is unclear. Three early fossil taxa are generally recognized, all from South Africa: Papio izodi, Papio robinsoni and Papio angusticeps. Because of their derived appearance, P. angusticeps and P. robinsoni have sometimes been considered subspecies of P. hamadryas and have been used as biochronological markers for the Plio-Pleistocene hominin sites where they are found.
We reexamined fossil Papio forms from across Africa with an emphasis on their distinguishing features and distribution. We find that P. robinsoni and P. angusticeps are distinct from each other in several cranial features, but overlap extensively in dental size. Contrary to previous assessments, no diagnostic cranio-mandibular material suggests these two forms co-occur, and dental variation at each site is comparable to that within P. h. ursinus, suggesting that only one form is present in each case. P izodi, however, may co-occur with P. robinsoni, or another Papio form, at Sterkfontein Member 4.
P izodi appears more primitive than P. robinsoni and P. angusticeps. P. robinsoni is slightly distinct from P. hamadryas subspecies in its combination of features while P. angusticeps might be included within one of the modern P. hamadryas varieties (i.e., P. h. angusticeps). No definitive Papio fossils are currently documented in eastern Africa until the Middle Pleistocene, pointing to southern Africa as the geographic place of origin for the genus. These results have implications for Plio-Pleistocene biochronology and baboon evolution.
Publication date: Available online 20 June 2018
Source: Journal of Human Evolution
Author(s): Doug M. Boyer, Stephanie A. Maiolino, Patricia A. Holroyd, Paul E. Morse, Jonathan I. Bloch
Euprimates are unusual among mammals in having fingers and toes with flat nails. While it seems clear that the ancestral stock from which euprimates evolved had claw-bearing digits, the available fossil record has not yet contributed a detailed understanding of the transition from claws to nails. This study helps clarify the evolutionary history of the second pedal digit with fossils representing the distal phalanx of digit two (dpII), and has broader implications for other digits. Among extant primates, the keratinized structure on the pedal dpII widely varies in form. Extant strepsirrhines and tarsiers have narrow, distally tapering, dorsally inclined nails (termed a 'grooming claws' for their use in autogrooming), while extant anthropoids have more typical nails that are wider and lack distal tapering or dorsal inclination. At least two fossil primate species thought to be stem members of the Strepsirrhini appear to have had grooming claws, yet reconstructions of the ancestral euprimate condition based on direct evidence from the fossil record are ambiguous due to inadequate fossil evidence for the earliest haplorhines. Seven recently discovered, isolated distal phalanges from four early Eocene localities in Wyoming (USA) closely resemble those of the pedal dpII in extant prosimians. On the basis of faunal associations, size, and morphology, these specimens are recognized as the grooming phalanges of five genera of haplorhine primates, including one of the oldest known euprimates (∼56 Ma), Teilhardina brandti. Both the phylogenetic distribution and antiquity of primate grooming phalanges now strongly suggest that ancestral euprimates had grooming claws, that these structures were modified from a primitive claw rather than a flat nail, and that the evolutionary loss of 'grooming claws' represents an apomorphy for crown anthropoids.
Publication date: Available online 19 June 2018
Source: Journal of Human Evolution
Author(s): Joel D. Irish, Shara E. Bailey, Debbie Guatelli-Steinberg, Lucas K. Delezene, Lee R. Berger
A new species of Homo, Homo naledi, was described in 2015 based on the hominin skeletal remains from the Dinaledi Chamber of the Rising Star cave system, South Africa. Subsequent craniodental comparative analyses, both phenetic and cladistic, served to support its taxonomic distinctiveness. Here we provide a new quantitative analysis, where up to 78 nonmetric crown and root traits of the permanent dentition were compared among samples of H. naledi (including remains from the recently discovered Lesedi Chamber) and eight other species from Africa: Australopithecus afarensis, Australopithecus africanus, Paranthropus boisei, Paranthropus robustus, Homo habilis, Homo erectus, Middle Pleistocene Homo sp., and Pleistocene and Holocene Homo sapiens. By using the mean measure of divergence distance statistic, phenetic affinities were calculated among samples to evaluate interspecific relatedness. The objective was to compare the results with those previously obtained, to assess further the taxonomic validity of the Rising Star hominin species. In accordance with earlier findings, H. naledi appears most similar dentally to the other African Homo samples. However, the former species is characterized by its retention and full expression of features relating to the main cusps, as well as the root numbers, with a near absence of accessory traits—including many that, based on various cladistic studies, are plesiomorphic in both extinct and extant African hominins. As such, the present findings provide additional support for the taxonomic validity of H. naledi as a distinct species of Homo.
Publication date: Available online 15 June 2018
Source: Journal of Human Evolution
Author(s): Mark Grabowski, Kevin G. Hatala, William L. Jungers
Many hypotheses regarding the paleobiology of the earliest possible hominins, Orrorin tugenensis and Ardipithecus ramidus, are dependent upon accurate body mass estimates for these taxa. While we have previously published body mass predictions for Orrorin and Ardipithecus, the accuracies of those estimates depend on the assumption that the postcranial skeletal dimensions and body masses of these taxa followed scaling patterns that were similar to those observed in modern humans. This assumption may not be correct because certain aspects of postcranial morphology in Orrorin and Ardipithecus differ from modern humans, and suggest that their overall body plans might be unique but more similar to modern non-human great apes than to modern humans. Here we present individual body mass predictions for O. tugenensis and Ar. ramidus assuming that they followed postcranial scaling patterns similar to those of chimpanzees. All estimates include individual prediction intervals as measures of uncertainty. In addition, we provide equations for predicting body mass from univariate postcranial measurements based on the largest sample (n = 25) yet compiled of common chimpanzee skeletons with known body masses, which is vital for calculating prediction intervals for individual fossils. Our results show that estimated body masses in Orrorin and Ardipithecus are generally larger when derived from a chimpanzee-like scaling pattern compared to estimates that assume a human-like pattern, though the prediction intervals of the two sets of estimates overlap. In addition, the more complete of the two known Orrorin femora has an overall scaling pattern that is more similar to common chimpanzees than to modern humans, supporting the application of a non-human great ape comparative model. Our new estimates fall near the male (Ardipithecus) average and in between the male and female averages (Orrorin) for wild-caught common chimpanzees. If a chimpanzee-like pattern of scaling between postcranial dimensions and body mass did exist in these earliest hominins, our results suggest the large body masses found in some early australopiths were already present in taxa near the origins of our lineage, and perhaps also in the Pan-Homo last common ancestor.
Publication date: Available online 14 June 2018
Source: Journal of Human Evolution
Author(s): Jason J. Head, Johannes Müller
The squamate fossil record from Kanapoi reveals generic to higher-order similarities with modern East African herpetofaunas. The record is derived from surface collection and screen washing, and consists primarily of isolated vertebrae with a few maxillary and mandibular elements. The most abundant remains are vertebrae of large-bodied Python that are morphologically similar to extant Python sebae, and vertebrae of Varanus cf. (Varanus niloticus + Varanus exanthematicus). Additional cranial and vertebral remains indicate the presence of lygosomine skinks, indeterminate Varanus, Viperidae, cf. Atractaspididae, and multiple colubrine morphotypes in the Kanapoi ecosystem. Despite similarities with modern herpetofaunas, the Kanapoi record lacks taxa common to other East African records, including agamids, chamaeleonids, amphisbaenians, the elapid Naja, and typhlopids. The overall composition of the Kanapoi squamate record is consistent with paleoenvironments similar to modern shrub savanna habitats. There are no indicators of canopied forest environments in squamate faunal composition. The fossil record of Kanapoi suggests that assembly of squamate faunas of modern East Africa was well underway by the late Neogene.
Publication date: Available online 7 June 2018
Source: Journal of Human Evolution
Author(s): Kenneth D. Rose, Rachel H. Dunn, Kishor Kumar, Jonathan M.G. Perry, Kristen A. Prufrock, Rajendra S. Rana, Thierry Smith
Several new fossil specimens from the Cambay Shale Formation at Tadkeshwar Lignite Mine in Gujarat document the presence of two previously unknown early Eocene primate species from India. A new species of Asiadapis is named based on a jaw fragment preserving premolars similar in morphology to those of A. cambayensis but substantially larger. Also described is an exceptionally preserved edentulous dentary (designated cf. Asiadapis, unnamed sp. nov.) that is slightly larger and much more robust than previously known Cambay Shale primates. Its anatomy most closely resembles that of Eocene adapoids, and the dental formula is the same as in A. cambayensis. A femur and calcaneus are tentatively allocated to the same taxon. Although the dentition is unknown, exquisite preservation of the dentary of cf. Asiadapis sp. nov. enables an assessment of masticatory musculature, function, and gape adaptations, as well as comparison with an equally well-preserved dentary of the asiadapid Marcgodinotius indicus, also from Tadkeshwar. The new M. indicus specimen shows significant gape adaptations but was probably capable of only weak bite force, whereas cf. Asiadapis sp. nov. probably used relatively smaller gapes but could generate relatively greater bite forces.
Sport-related concussion and repetitive head impact exposure in contact sports continue to receive increased attention in public and medical spheres. The Concussion Assessment, Research and Education (CARE) Consortium, a multicenter cooperative, was established to study the natural history of concussion in National Collegiate Athletic Association (NCAA) collegiate student-athletes across 29 colleges and universities in the United States. The purpose of this investigation is to provide normative data from the CARE Consortium and evaluate for differences between sport categories.
NCAA student-athletes were evaluated annually for general demographics and sport-specific characteristics before the start of the competitive season. We collected demographic and medical history information and evaluated each student-athlete's neurocognitive function, neurological status, postural stability, and self-reported symptoms. Sports were categorized by the amount of contact typically associated with the sport (i.e., contact, limited contact, non-contact). Comparisons between the three sport categories for the evaluated variables were made using linear or zero inflated negative binomial regression models adjusted for gender, concussion history, and household income.
Over a 2-year period (August 2014–July 2016), 15,681 NCAA athletes completed preseason evaluations. Overall, 53% of the athletes were in the contact sport group, 31% were in the limited contact group and 17% were in the non-contact group. After adjusting for covariates, there were statistically significant differences found between athlete groups, although the differences and effect sizes were small and not clinically significant. The contact sport group had better scores on Immediate Post-Concussion Assessment Testing (ImPACT®) visual and verbal memory, Sport Concussion Assessment Tool (SCAT) symptom checklist, and Brief Symptom Inventory–18 (BSI-18), but slower ImPACT reaction time and worse scores on Standardized Assessment of Concussion (SAC). Further, the data indicate that some ImPACT score distributions were noticeably different from those presented in the technical manual.
In this large, racially and socio-economically diverse cohort of male and female college athletes, we found no evidence that student-athletes participating in contact sports have clinically meaningful deficits in pre-season cognitive and balance testing. They also did not report significantly more symptoms of psychological distress when compared with student-athletes in non-contact or limited contact sports. In addition, the data suggest potential limitations when using published ImPACT norms when evaluating injured athletes.
Publication date: Available online 7 June 2018
Source: Journal of Human Evolution
Author(s): Raef Minwer-Barakat, Judit Marigó, Salvador Moyà-Solà
The scarce primate remains from the late Eocene locality of Roc de Santa (Central Pyrenees, NE Spain) were first documented in 1975. This material included a mandibular fragment with P3-M2 and a maxillary fragment with P3-M3 assigned to Adapis magnus (later transferred to the genus Leptadapis), and an isolated M3 attributed to Necrolemur antiquus. However, these specimens were never described in detail. We have thoroughly studied these specimens, with the exception of the mandibular fragment, which has been lost. The maxillary fragment is much smaller than in Leptadapis magnus and shows clear morphological differences from that species; this specimen is assigned to Microchoerus hookeri. Similarly, the isolated M3 resembles that of M. hookeri in size and morphology, and can therefore be attributed to this taxon. In addition, we describe an upper incisor never reported previously, which can also be allocated to M. hookeri, representing the first description of this tooth for the species. Therefore, we conclude that the previous taxonomic determinations were mistaken and all the available primate specimens from Roc de Santa can be confidently assigned to the species M. hookeri, previously described from the same-age localities of Sossís, Spain, and Eclépens-B, Switzerland.
Publication date: Available online 5 June 2018
Source: Journal of Human Evolution
Author(s): Sergio Jarillo, Alan Fridlund, Carlos Crivelli, Jose-Miguel Fernández-Dols, James A. Russell
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s): Erin Marie Williams-Hatala, Kevin G. Hatala, McKenzie Gordon, Alastair Key, Margaret Kasper, Tracy L. Kivell
It is widely agreed that biomechanical stresses imposed by stone tool behaviors influenced the evolution of the human hand. Though archaeological evidence suggests that early hominins participated in a variety of tool behaviors, it is unlikely that all behaviors equally influenced modern human hand anatomy. It is more probable that a behavior's likelihood of exerting a selective pressure was a weighted function of the magnitude of stresses associated with that behavior, the benefits received from it, and the amount of time spent performing it. Based on this premise, we focused on the first part of that equation and evaluated magnitudes of stresses associated with stone tool behaviors thought to have been commonly practiced by early hominins, to determine which placed the greatest loads on the digits. Manual pressure data were gathered from 39 human subjects using a Novel Pliance® manual pressure system while they participated in multiple Plio-Pleistocene tool behaviors: nut-cracking, marrow acquisition with a hammerstone, flake production with a hammerstone, and handaxe and flake use. Manual pressure distributions varied significantly according to behavior, though there was a tendency for regions of the hand subject to the lowest pressures (e.g., proximal phalanges) to be affected less by behavior type. Hammerstone use during marrow acquisition and flake production consistently placed the greatest loads on the digits collectively, on each digit and on each phalanx. Our results suggest that, based solely on the magnitudes of stresses, hammerstone use during marrow acquisition and flake production are the most likely of the assessed behaviors to have influenced the anatomical and functional evolution of the human hand.
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s): Tsuyoshi Ito, Yung-jo Lee, Takeshi D. Nishimura, Mikiko Tanaka, Jong-yoon Woo, Masanaru Takai
Little is known about the biogeographical and evolutionary histories of macaques (Macaca spp.) in East Asia because the phylogenetic positions of fossil species remain unclear. Here we examined the zygomaxillary remains of a fossil macaque (M. cf. robusta) from the Durubong Cave Complex, South Korea, that dates back to the late Middle to Late Pleistocene, to infer its phylogenetic relationship to extant species. We took 195 fixed- and semi-landmarks from the zygomaxillary regions of the fossil specimen and from 147 specimens belonging to 14 extant species. We then conducted a generalized Procrustes analysis followed by a multivariate statistical analysis to evaluate the phenetic affinities of the fossil to the extant species and reconstructed the most parsimonious phylogenetic tree using a phylogenetic morphometric approach. We found that the fossil was most similar to Macaca fuscata (Japanese macaque) in the zygomaxillary morphospace although it was at the limit of the range of variation for this species. The second closest in the morphospace was the continental Macaca mulatta (rhesus macaque). Parsimonious reconstruction confirmed that the fossil was most closely related to M. fuscata, even after controlling for the effects of allometry. These findings suggest that in the late Middle to Late Pleistocene, close relatives of M. fuscata that looked like the extant species were distributed on the Korean Peninsula, where no species of macaques are found today. Thus, some morphological characteristics of M. fuscata may have developed before its ancestor dispersed into the Japanese archipelago.
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s):
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s): Karen L. Baab, Lynn E. Copes, Devin L. Ward, Nora Wells, Frederick E. Grine
The systemic robusticity hypothesis links the thickness of cortical bone in both the cranium and limb bones. This hypothesis posits that thick cortical bone is in part a systemic response to circulating hormones, such as growth hormone and thyroid hormone, possibly related to physical activity or cold climates. Although this hypothesis has gained popular traction, only rarely has robusticity of the cranium and postcranial skeleton been considered jointly. We acquired computed tomographic scans from associated crania, femora and humeri from single individuals representing 11 populations in Africa and North America (n = 228). Cortical thickness in the parietal, frontal and occipital bones and cortical bone area in limb bone diaphyses were analyzed using correlation, multiple regression and general linear models to test the hypothesis. Absolute thickness values from the crania were not correlated with cortical bone area of the femur or humerus, which is at odds with the systemic robusticity hypothesis. However, measures of cortical bone scaled by total vault thickness and limb cross-sectional area were positively correlated between the cranium and postcranium. When accounting for a range of potential confounding variables, including sex, age and body mass, variation in relative postcranial cortical bone area explained ∼20% of variation in the proportion of cortical cranial bone thickness. While these findings provide limited support for the systemic robusticity hypothesis, cranial cortical thickness did not track climate or physical activity across populations. Thus, some of the variation in cranial cortical bone thickness in modern humans is attributable to systemic effects, but the driving force behind this effect remains obscure. Moreover, neither absolute nor proportional measures of cranial cortical bone thickness are positively correlated with total cranial bone thickness, complicating the extrapolation of these findings to extinct species where only cranial vault thickness has been measured.
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s): Craig S. Feibel, Bernard Wood
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s): Robert C. Power, Domingo C. Salazar-García, Mauro Rubini, Andrea Darlas, Katerina Harvati, Michael Walker, Jean-Jacques Hublin, Amanda G. Henry
The ecology of Neanderthals is a pressing question in the study of hominin evolution. Diet appears to have played a prominent role in their adaptation to Eurasia. Based on isotope and zooarchaeological studies, Neanderthal diet has been reconstructed as heavily meat-based and generally similar across different environments. This image persists, despite recent studies suggesting more plant use and more variation. However, we have only a fragmentary picture of their dietary ecology, and how it may have varied among habitats, because we lack broad and environmentally representative information about their use of plants and other foods. To address the problem, we examined the plant microremains in Neanderthal dental calculus from five archaeological sites representing a variety of environments from the northern Balkans, and the western, central and eastern Mediterranean. The recovered microremains revealed the consumption of a variety of non-animal foods, including starchy plants. Using a modeling approach, we explored the relationships among microremains and environment, while controlling for chronology. In the process, we compared the effectiveness of various diversity metrics and their shortcomings for studying microbotanical remains, which are often morphologically redundant for identification. We developed Minimum Botanical Units as a new way of estimating how many plant types or parts are present in a microbotanical sample. In contrast to some previous work, we found no evidence that plant use is confined to the southern-most areas of Neanderthal distribution. Although interpreting the ecogeographic variation is limited by the incomplete preservation of dietary microremains, it is clear that plant exploitation was a widespread and deeply rooted Neanderthal subsistence strategy, even if they were predominately game hunters. Given the limited dietary variation across Neanderthal range in time and space in both plant and animal food exploitation, we argue that vegetal consumption was a feature of a generally static dietary niche.
Publication date: June 2018
Source: Journal of Human Evolution, Volume 119
Author(s): Alexandria Peterson, Elicia F. Abella, Frederick E. Grine, Mark F. Teaford, Peter S. Ungar
The importance of diet in primate ecology has motivated the use of a variety of methods to reconstruct dietary habits of extinct hominin taxa. Dental microwear is one such approach that preserves evidence from consumed food items. This study is based on 44 specimens of Australopithecus africanus from Makapansgat and Sterkfontein, and 66 specimens of Paranthropus robustus from Swartkrans, Kromdraai and Drimolen. These samples enable examination of potential differences between the two assemblages of A. africanus, and among the various assemblages of P. robustus in relation to the paleoenvironmental reconstructions that have been proffered for each fossil site. Sixteen microwear texture variables were recorded for each specimen from digital elevation models generated using a white-light confocal profiler. Only two of these differ significantly between the Makapansgat and Sterkfontein samples of A. africanus. None of the microwear texture variables differs significantly among the samples of P. robustus. On the other hand, P. robustus has significantly higher values than A. africanus for 11 variables related to feature complexity, size, and depth; P. robustus exhibits rougher surfaces that comprise larger, deeper features. In contrast, A. africanus has smoother, simpler wear surfaces with smaller, shallower and more anisotropic features. As for possible habitat differences among the various sites, only a relatively small number of subtle differences are evident between the specimens of A. africanus from Makapansgat and Sterkfontein, and there are none among the specimens of P. robustus from various deposits. As such, it is reasonable to conclude that, while subtle differences in microwear textures may reflect differences in background habitats, the wear fabric differences between P. robustus and A. africanus are most reasonably interpreted as having been driven by dietary differences.
Publication date: Available online 31 May 2018
Source: Journal of Human Evolution
Author(s): Feng Li, Christopher J. Bae, Christopher B. Ramsey, Fuyou Chen, Xing Gao
Due to the presence of multiple partial modern human skeletons thought to have been interred along with a diversity of evidence of symbolic behavior, Zhoukoudian Upper Cave (ZKD UC; formally "Choukoutien") from northern China has long been a critical site for understanding Late Quaternary human evolution and particularly the role eastern Asia played. Unfortunately, uncertainty regarding ZKD UC's chronology has long hindered determination of its importance in the debate over modern human origins. This situation has been particularly problematic because dates from the primary archaeological layers of ZKD UC have ranged from the Late Pleistocene to the Early Holocene (∼34–10 ka), with clearly different implications depending on which age is used. Here, we present a new set of accelerator mass spectrometry radiocarbon dating results from ZKD UC. Based on this new set of dates and further re-evaluations of the previous dating analyses, archaeological materials, published excavation reports and stratigraphy, we conclude that the ZKD UC archaeological layers minimally date to 35.1–33.5 ka. Given the similarities between the human fossils and archaeology between ZKD UC and western Eurasia, it is likely that the ZKD UC human foragers were part of dispersal events across northern Eurasia toward Siberia and eventually reaching into northern China.
Publication date: Available online 29 May 2018
Source: Journal of Human Evolution
Author(s): Aurélien Mounier, Maria Correia, Frances Rivera, Federica Crivellaro, Ronika Power, Joe Jeffery, Alex Wilshaw, Robert A. Foley, Marta Mirazón Lahr
Africa is the birthplace of the species Homo sapiens, and Africans today are genetically more diverse than other populations of the world. However, the processes that underpinned the evolution of African populations remain largely obscure. Only a handful of late Pleistocene African fossils (∼50-12 Ka) are known, while the more numerous sites with human fossils of early Holocene age are patchily distributed. In particular, late Pleistocene and early Holocene human diversity in Eastern Africa remains little studied, precluding any analysis of the potential factors that shaped human diversity in the region, and more broadly throughout the continent. These periods include the Last Glacial Maximum (LGM), a moment of extreme aridity in Africa that caused the fragmentation of population ranges and localised extinctions, as well as the 'African Humid Period', a moment of abrupt climate change and enhanced connectivity throughout Africa. East Africa, with its range of environments, may have acted as a refugium during the LGM, and may have played a critical biogeographic role during the heterogene`ous environmental recovery that followed. This environmental context raises a number of questions about the relationships among early Holocene African populations, and about the role played by East Africa in shaping late hunter-gatherer biological diversity. Here, we describe eight mandibles from Nataruk, an early Holocene site (∼10 Ka) in West Turkana, offering the opportunity of exploring population diversity in Africa at the height of the 'African Humid Period'. We use 3D geometric morphometric techniques to analyze the phenotypic variation of a large mandibular sample. Our results show that (i) the Nataruk mandibles are most similar to other African hunter-fisher-gatherer populations, especially to the fossils from Lothagam, another West Turkana locality, and to other early Holocene fossils from the Central Rift Valley (Kenya); and (ii) a phylogenetic connection may have existed between these Eastern African populations and some Nile Valley and Maghrebian groups, who lived at a time when a Green Sahara may have allowed substantial contact, and potential gene flow, across a vast expanse of Northern and Eastern Africa.
Publication date: Available online 28 May 2018
Source: Journal of Human Evolution
Author(s): Katja Douze, Anne Delagnes, Veerle Rots, Brad Gravina
Sahle and Braun's (in press) recent comments on our identification (Douze and Delagnes, 2016) of diachronic trends in Middle Stone Age point traditions in several lithic assemblages from the sites of Gademotta and Kulkuletti (Ethiopia) focuses on pointed tool function rather than the gradual technological shifts we observed between sites. Here we address several of what we consider to be inaccuracies and misinterpretations concerning our work with the Gademotta and Kulkuletti lithic assemblages (Douze, 2012, 2014), more specifically, Sahle and Braun's (in press) interpretation of the tranchet blow technique. This discussion is inseparable from a critical review of the evidence advanced by Sahle and Braun to support projectile technology being present in the Gademotta Formation as early as >279 ka.
Publication date: Available online 24 May 2018
Source: Journal of Human Evolution
Author(s): Biren A. Patel, Tea Jashashvili, Stephanie H. Bui, Kristian J. Carlson, Nicole L. Griffin, Ian J. Wallace, Caley M. Orr, Randall L. Susman
When measured as a ratio of mean midshaft diameter to bone length, the OH 8 fossil hominin foot exhibits a metatarsal (Mt) robusticity pattern of 1 > 5 > 3 > 4 > 2, which differs from the widely perceived "common" modern human pattern (1 > 5 > 4 > 3 > 2); African apes generally exhibit a third pattern (1 > 2 > 3 > 4 > 5). Largely because of the relative ranking of Mt2 and Mt5, OH 8 metatarsals structurally resemble the pattern exhibited by bipedal humans more than the pattern of quadrupedal and climbing African apes. Considering only these three phenotypes, however, discounts the potentially important functional implications of variation in modern human (and African ape) metatarsal robusticity patterns, suggesting that they are not useful for interpreting the specific biomechanics of a bipedal gait in fossils (i.e., whether it was modern human-like or not). Using computed tomography scans to quantify metatarsal midshaft cross-sectional geometry in a large sample of Homo (n=130), Gorilla (n=44) and Pan (n=80), we documented greater variation in metatarsal robusticity patterns than previously recognized in all three groups. While apes consistently show a 1 > 2 > 3 > 4 > 5 pattern in our larger sample, there does not appear to be a similarly precise single "common" human pattern. Rather, human metatarsals converge towards a 1 > 4/5 > 2/3 pattern, where metatarsals 4 and 5, and metatarsals 2 and 3, often "flip" positions relative to each other depending on the variable examined. After reassessing what a "common" human pattern could be based on a larger sample, the previously described OH 8 pattern of 1 > 5 > 3 > 4 > 2 is only observed in some humans (<6%) and almost never in apes (<0.5%). Although this suggests an overall greater similarity to (some) humans than to any ape in loading of the foot, the relatively rare frequency of these humans in our sample underscores potential differences in loading experienced by the medial and lateral columns of the OH 8 foot compared to modern humans.
Publication date: Available online 5 July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Author(s): Ioanna Pavlaki, France Docquier, Igor Chernukhin, Georgia Kita, Svetlana Gretton, Christopher T. Clarkson, Vladimir B. Teif, Elena Klenova
CTCF is an evolutionarily conserved and ubiquitously expressed architectural protein regulating a plethora of cellular functions via different molecular mechanisms. CTCF can undergo a number of post-translational modifications which change its properties and functions. One such modifications linked to cancer is poly(ADP-ribosyl)ation (PARylation). The highly PARylated CTCF form has an apparent molecular mass of 180 kDa (referred to as CTCF180), which can be distinguished from hypo- and non-PARylated CTCF with the apparent molecular mass of 130 kDa (referred to as CTCF130). The existing data accumulated so far have been mainly related to CTCF130. However, the properties of CTCF180 are not well understood despite its abundance in a number of primary tissues. In this study we performed ChIP-seq and RNA-seq analyses in human breast cells 226LDM, which display predominantly CTCF130 when proliferating, but CTCF180 upon cell cycle arrest. We observed that in the arrested cells the majority of sites lost CTCF, whereas fewer sites gained CTCF or remain bound (i.e. common sites). The classical CTCF binding motif was found in the lost and common, but not in the gained sites. The changes in CTCF occupancies in the lost and common sites were associated with increased chromatin densities and altered expression from the neighboring genes. Based on these results we propose a model integrating the CTCF130/180 transition with CTCF-DNA binding and gene expression changes. This study also issues an important cautionary note concerning the design and interpretation of any experiments using cells and tissues where CTCF180 may be present.
Publication date: Available online 3 July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Author(s): Veijo Nurminen, Antonio Neme, Sabine Seuter, Carsten Carlberg
The micronutrient vitamin D significantly modulates the human epigenome via enhancing genome-wide the rate of accessible chromatin and vitamin D receptor (VDR) binding. This study focuses on histone marks of active chromatin at promoter and enhancer regions and investigates, whether these genomic loci are sensitive to vitamin D. The epigenome of THP-1 human monocytes contains nearly 23,000 sites with H3K4me3 histone modifications, 550 of which sites are significantly (p < 0.05) modulated by stimulation with the VDR ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). H3K27ac histone modifications mark active chromatin and 2473 of 45,500 sites are vitamin D sensitive. The two types of ligand-dependent histone marks allow to distinguish promoter and enhancer regulation by vitamin D, respectively. Transcription start site overlap is the prime attribute of ligand-dependent H3K4me3 marks, while VDR co-location is the top ranking parameter describing 1,25(OH)2D3-sensitive H3K27ac marks at enhancers. A categorization of 1,25(OH)2D3-sensitive histone marks by machine learning algorithms - using the attributes overall peak strength and ligand inducibility - highlights 260 and 287 regions with H3K4me3 and H3K27ac modifications, respectively. These loci are found at the promoter regions of 59 vitamin D target genes and their associated enhancers. In this way, ligand-dependent histone marks provide a link of the effects of 1,25(OH)2D3 on the epigenome with previously reported mRNA expression changes of vitamin D target genes. In conclusion, the human epigenome responds also on the level of histone modifications to 1,25(OH)2D3 stimulation. This allows a more detailed understanding of vitamin D target gene regulation.
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s):
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): Chun-Bo Song, Wei Shan, Ying-Ying Yang, Xiao-Li Tan, Zhong-Qi Fan, Jian-Ye Chen, Wang-Jin Lu, Jian-Fei Kuang
The biological processes involved in banana fruit ripening are extremely complex and modulated by a number of genes such as transcription factors (TFs). Although TFs like MADS, ERF and NAC are implicated in controlling banana ripening, little is known about other TFs such as TCP in this process. In this work, 25 MaTCPs named MaTCP1 to MaTCP25 were characterized from our previously reported transcriptomes related to banana ripening. Expression analysis revealed that these MaTCPs displayed differential expression patterns during the progression of banana ripening. Particularly, MaTCP5, MaTCP19 and MaTCP20 were ethylene-inducible and nuclear-localized, with MaTCP5 and MaTCP20 acting as transcriptional activators while MaTCP19 being a transcriptional inhibitor. Moreover, MaTCP5 and MaTCP20 promoted the transcription of MaXTH10/11 that may play a role in fruit softening during banana ripening, whereas MaTCP19 repressed their transcription, by directly binding to their promoters. Importantly, protein-protein interaction assays demonstrated that MaTCP20 physically interacts with MaTCP5 and MaTCP19 to form heterodimers in vitro and in vivo, and these protein complexes affects their transcriptional activities in regulating the target genes. Taken together, our results provide an overview of the interactions between MaTCPs in controlling the ripening-associated genes and lay a foundation for further investigation of MaTCP gene family in regulating banana fruit ripening.
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): Eunsun Jung, Youngmo Seong, Bohyun Jeon, Young-Soo Kwon, Hoseok Song
MicroRNAs (miRNAs) of the miR-17-92 cluster are overexpressed in human cancers, and their enforced expression is tumorigenic in mouse models. A number of genes are reported to be targets of these miRNAs and are implicated in their tumorigenic potential. However, the mode of action by miRNAs suggests that global analysis of their targets is required to understand their cellular roles. In this study, we globally analyzed AGO2-bound mRNAs and found that the miR-17-92 miRNAs coherently repress multiple targets involved in the destabilization of mRNA. While the miRNAs repress the expression of their targets, they increase stability and lengthen the poly-A tails of non-target mRNAs. Furthermore, the expression of BTG3, TOB1, CSNK1A1 and ANKRD52 is negatively correlated with the expression of the miR-17-92 cluster in cancer cell lines. Our results suggest that the miR-17-92 miRNAs promote tumorigenesis not only by repression of key regulators, but also by posttranscriptional increases of global gene expression.
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): A. Sorrentino, M. Rienzo, A. Ciccodicola, A. Casamassimi, C. Abbondanza
PRDM2/RIZ is a member of a superfamily of histone/protein methyltransferases (PRDMs), which are characterized by the conserved N-terminal PR domain, with methyltransferase activity and zinc finger arrays at the C-terminus. Similar to other family members, two main protein types, known as RIZ1 and RIZ2, are produced from the PRDM2 locus differing by the presence or absence of the PR domain. The imbalance in their respective amounts may be an important cause of malignancy, with the PR-positive isoform commonly lost or downregulated and the PR-negative isoform always being present at higher levels in cancer cells. Interestingly, the RIZ1 isoform also represents an important target of estradiol action downstream of the interaction with hormone receptor. Furthermore, the imbalance between the two products could also be a molecular basis for other human diseases. Thus, understanding the molecular mechanisms underlying PRDM2 function could be useful in the pathophysiological context, with a potential to exploit this information in clinical practice.
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): Jin Kang, Yea Woon Kim, AeRi Kim
Histone variants H3.3 and H2A.Z are often enriched in enhancers and transcriptionally active genes. However, the incorporation dynamics of these variants and the mechanisms of their incorporation are unclear. Here, we examined the distribution of H3.3 and H2A.Z in the human β-globin locus and analyzed their incorporation dynamics during transcription activation. Locus control region hypersensitive sites (LCR HSs), acting as enhancers, and active globin genes were enriched by H3.3 and H2A.Z in erythroid K562 cells, but inactive globin genes were not. Both variants were dynamically incorporated into the β-globin locus after transcription induction in MEL/ch11 cells, and prior to gene transcription the LCR HSs became enriched with the variants. In the activated β-globin gene, H3.3 was highly incorporated during transcription, whereas H2A.Z incorporation appeared to precede it. To further explore the relationship between gene transcription and variant incorporation, we deleted the LCR HS3 enhancer or the β-globin proximal promoter from the β-globin locus using the CRISPR-Cas9 genome editing system. H2A.Z was incorporated into the β-globin gene in the locus lacking promoter, even though the β-globin gene transcription was abolished by these deletions. However, H3.3 incorporation was reduced in the untranscribed β-globin gene. These results suggest that H3.3 and H2A.Z are systematically incorporated into the LCR enhancer and β-globin gene as part of transcription activation, but that their incorporation is carried out via different mechanisms.
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): Anna M. Mleczko, Piotr Celichowski, Kamilla Bąkowska-Żywicka
Ribosome-associated noncoding (ranc) RNAs are a novel class of short regulatory RNAs with functions and origins that have not been well studied. In this present study, we functionally characterized the molecular activity of Saccharomyces cerevisiae transfer RNA (tRNA)-derived fragments (tRFs) during protein biosynthesis. Our results indicate ribosome-associated tRFs derived from both 5′ (ranc-5′-tRFs) and 3′-part of tRNAs (ranc-3′-tRFs) have regulatory roles during translation. We demonstrated five 3′-tRFs and one 5′-tRF associate with a small ribosomal subunit and aminoacyl-tRNA synthetases (aa-RSs) in yeast. Furthermore, we discovered that four yeast aa-RSs interact directly with yeast ribosomes. tRFs interactions with ribosome-associated aa-RSs correlate with impaired efficiency of tRNA aminoacylation.
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): Ankita Shrestha, Ahamed Khan, Dipti Ranjan Mishra, Kashyap Bhuyan, Bhabani Sahoo, Indu B. Maiti, Nrisingha Dey
Publication date: July 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7
Author(s): Matías I. Hepp, David Escobar, Carlos Farkas, Viviana E. Hermosilla, Claudia Álvarez, Roberto Amigo, José L. Gutiérrez, Ariel F. Castro, Roxana Pincheira
SALL2 is a transcription factor involved in development and disease. Deregulation of SALL2 has been associated with cancer, suggesting that it plays a role in the disease. However, how SALL2 is regulated and why is deregulated in cancer remain poorly understood. We previously showed that the p53 tumor suppressor represses SALL2 under acute genotoxic stress. Here, we investigated the effect of Histone Deacetylase Inhibitor (HDACi) Trichostatin A (TSA), and involvement of Sp1 on expression and function of SALL2 in Jurkat T cells. We show that SALL2 mRNA and protein levels were enhanced under TSA treatment. Both, TSA and ectopic expression of Sp1 transactivated the SALL2 P2 promoter. This transactivation effect was blocked by the Sp1-binding inhibitor mithramycin A. Sp1 bound in vitro and in vivo to the proximal region of the P2 promoter. TSA induced Sp1 binding to the P2 promoter, which correlated with dynamic changes on H4 acetylation and concomitant recruitment of p300 or HDAC1 in a mutually exclusive manner. Our results suggest that TSA-induced Sp1-Lys703 acetylation contributes to the transcriptional activation of the P2 promoter. Finally, using a CRISPR/Cas9 SALL2-KO Jurkat-T cell model and gain of function experiments, we demonstrated that SALL2 upregulation is required for TSA-mediated cell death. Thus, our study identified Sp1 as a novel transcriptional regulator of SALL2, and proposes a novel epigenetic mechanism for SALL2 regulation in Jurkat-T cells. Altogether, our data support SALL2 function as a tumor suppressor, and SALL2 involvement in cell death response to HDACi.
Publication date: Available online 30 June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Author(s): Alban Chauderlier, Melissa Gilles, Andrea Spolcova, Raphaelle Caillierez, Maggy Chwastyniak, Michel Kress, Herve Drobecq, Eliette Bonnefoy, Florence Pinet, Dominique Weil, Luc Buée, Marie-Christine Galas, Bruno Lefebvre
Tauopathies, such as Alzheimer's disease, are characterized by intracellular aggregates of insoluble Tau proteins. Originally described as a microtubule binding protein, recent studies demonstrated additional physiological roles for Tau. The fact that a single protein can regulate multiple cellular functions has posed challenge in terms of understanding mechanistic cues behind the pathology. Here, we used tandem-affinity purification methodology coupled to mass spectrometry to identify novel interaction partners. We found that Tau interacts with DDX6, a DEAD box RNA helicase involved in translation repression and mRNA decay as well as in the miRNA pathway. Our results demonstrate that Tau increases the silencing activity of the miRNA let-7a, miR-21 and miR-124 through DDX6. Importantly, Tau mutations (P301S, P301L) found in the inherited tauopathies, frontotemporal dementia and parkinsonism linked to chromosome 17, disrupt Tau/DDX6 interaction and impair gene silencing by let-7a. Altogether, these data demonstrated a new unexpected role for Tau in regulating miRNA activity.
Publication date: Available online 30 June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Author(s): Robert Liefke, Kristin Bokelmann, B. Michael Ghadimi, Sebastian Dango
Obesity is characterized by the excess of body fat leading to impaired health. Abdominal fat is particularly harmful and is associated with cardiovascular and metabolic diseases and cancer. In contrast, subcutaneous fat is generally considered less detrimental. The mechanisms that establish the cellular characteristics of these distinct fat types in humans are not fully understood. Here, we explored whether differences of their gene regulatory mechanisms can be investigated in vitro. For this purpose, we in vitro differentiated human visceral and subcutaneous pre-adipocytes into mature adipocytes and obtained their gene expression profiles and genome-wide H3K4me3, H3K9me3 and H3K27ac patterns. Subsequently, we compared those data with public gene expression data from visceral and subcutaneous fat tissues. We found that the in vitro differentiated adipocytes show significant differences in their transcriptional landscapes, which correlate with biological pathways that are characteristic for visceral and subcutaneous fat tissues, respectively. Unexpectedly, visceral adipocyte enhancers are rich on motifs for transcription factors involved in the Hippo-YAP pathway, cell growth and inflammation, which are not typically associated with adipocyte function. In contrast, enhancers of subcutaneous adipocytes show enrichment of motifs for common adipogenic transcription factors, such as C/EBP, NFI and PPARγ, implicating substantially disparate gene regulatory networks in visceral and subcutaneous adipocytes. Consistent with the role in obesity, predominantly the histone modification pattern of visceral adipocytes is linked to obesity-associated diseases. Thus, this work suggests that the properties of visceral and subcutaneous fat tissues can be studied in vitro and provides preliminary insights into their gene regulatory processes.
Publication date: Available online 22 June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Author(s): Zilong Li, Baoyu Chen, Xinyu Weng, Liming Yu, Mingzi Song, Mingming Fang, Junli Guo, Yong Xu
Thrombomodulin (TM, encoded by the THBD gene) expressed in vascular endothelial cells plays pivotal roles maintaining the equilibrium of coagulation and anti-coagulation. TM levels can be regulated at the transcriptional level although the epigenetic mechanism is underexplored. Here we report that transcriptional activation of TM in both immortalized vascular endothelial cells (EAhy926) and primary human aortic endothelial cells (HAEC) by all-trans retinoic acid (RA) paralleled accumulation of trimethylated histone H3K4, a prominent marker for active chromatin, surrounding the THBD promoter. RA treatment up-regulated the expression of SETD1A (SET1), a dedicated H3K4 methyltransferase, and augmented SETD1A occupancies on the THBD promoter. Further analysis revealed that the sequence-specific transcription factor Kruppel-like factor 4 (KLF4) interacted with and recruited SETD1A to the THBD promoter. Interestingly, SETD1A was recruited to the KLF4 promoter by retinoic acid receptor (RAR) and mediated the up-regulation of KLF4 expression by RA stimulation. In summary, our data illustrate a previously unrecognized pathway in which SETD1A contributes to RA-induced TM expression in vascular endothelial cells by modulating the activity and expression of KLF4.
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s): Qian-Feng Li, Jun Lu, Jia-Wen Yu, Chang-Quan Zhang, Jun-Xian He, Qiao-Quan Liu
BZR1 and BES1 are key transcription factors of brassinosteroid (BR) signaling and represent the integration node of numerous signaling cascades. Their direct target genes have been identified, and BZR1/BES1-DNA interactions have been experimentally verified. Importantly, BZR1/BES1 also integrate different growth and development events via direct protein-protein interactions. For instance, DELLAs, PIFs, ARF6, and PKL, all directly interact with BZR1/BES1, forming a BZR1/BES1-centered regulatory network to coordinate cell elongation. By dissecting various BZR1/BES1-mediated BR responses, the concept that BZR1/BES1 act as an integration hub in multisignal-regulated plant growth and development was developed. The regulation of BZR1/BES1 is dynamic and multifaceted, including phosphorylation status, activity, and stability. Moreover, certain epigenetic modification mechanisms are involved in BZR1/BES1's regulation of gene expression. Herein, we review recent advances in BZR1/BES1-mediated molecular connections between BR and other pathways, highlighting the central role of the BZR1/BES1 interactome in optimizing plant growth and development.
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s):
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s): Radha Charan Dash, Angela M. Zaino, M. Kyle Hadden
The binding affinity between the histone 3 (H3) tail and the ADD domain of ATRX (ATRXADD) increases with the subsequent addition of methyl groups on lysine 9 on H3. To improve our understanding of how the difference in methylation state affects binding between H3 and the ATRXADD, we adopted a metadynamic approach to explore the recognition mechanism between the two proteins and identify the key intermolecular interactions that mediate this protein-peptide interaction (PPI). The non-methylated H3 peptide is recognized only by the PHD finger of ATRXADD while mono-, di-, and trimethylated H3 is recognized by both the PHD and GATA-like zinc finger of the domain. Furthermore, water molecules play an important role in orienting the lysine 9 anchor towards the GATA-like zinc finger, which results in stabilizing the lysine 9 binding pocket on ATRXADD. We compared our computational results against experimentally determined NMR and X-ray structures by demonstrating the RMSD, order parameter S2 and hydration number of the complex. The metadynamics data provide new insight into roles of water-bridges and the mechanisms through which K9 hydration stabilizes the H3K9me3:ATRXADD PPI, providing context for the high affinity demonstrated between this protein and peptide.
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s): Hanane Hadj-Moussa, Samantha M. Logan, Brad A. Seibel, Kenneth B. Storey
At night, Humboldt squid (Dosidicus gigas) rise to the ocean's surface to feed, but come morning, they descend into the ocean's oxygen minimum zone where they can avoid predators but must deal with severe hypoxia, high pressure, and very cold water. To survive this extreme environment, squid use various adaptations to enter a hypometabolic state characterized by metabolic rate suppression by 35–52%, relative to normoxic conditions. The molecular mechanisms facilitating this metabolic flexibility have yet to be elucidated in hypometabolic squid. Herein, we report the first investigation of the role of microRNAs, a rapid and reversible post-transcriptional master regulator of virtually all biological functions, in cephalopods. We examined expression levels of 39 highly-conserved invertebrate microRNAs in D. gigas brain, mantle muscle, and branchial heart, comparing hypoxic and normoxic conditions. Hypoxia-inducible microRNAs are potentially involved in facilitating neuroprotection, anti-apoptosis, and regenerative mechanisms in brain; inhibiting apoptosis and cell proliferation while conserving energy in heart; and limiting damage by reactive oxygen species and apoptosis in muscle. Rather than orchestrate global metabolic rate depression, the majority of hypoxia-inducible microRNAs identified are involved in promoting cytoprotective mechanisms, suggesting a regulatory role for microRNA in hypoxic marine invertebrates that sets the stage for mechanistic analyses.
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s): Abhijit S. Deshmukh, Pallabi Mitra, Ashok Kolagani, Rajkumar Gurupwar
Cyclin-dependent kinases are an essential part of eukaryotic transcriptional machinery. In Apicomplexan parasites, the role and relevance of the kinases in the multistep process of transcription seeks more attention given the absence of full repertoire of canonical Cdks and cognate cyclin partners. In this study, we functionally characterize T. gondii Cdk-related kinase 9 (TgCrk9) showing maximal homology to eukaryotic Cdk9. An uncanonical cyclin, TgCyclin L, colocalizes with TgCrk9 in the parasite nucleus and co-immunoprecipitate, could activate the kinase in-vitro. We identify two threonines in conserved T-loop domain of TgCrk9 that are important for its activity. The activated TgCrk9 phosphorylates C-terminal domain (CTD) of TgRpb1, the largest subunit of RNA polymerase II highlighting its role in transcription. Selective chemical inhibition of TgCrk9 affected serine 2 phosphorylation in the heptapeptide repeats of TgRpb1-CTD towards 3′ end of genes consistent with a possible role in transcription elongation. Interestingly, TgCrk9 kinase activity is regulated by the upstream TgCrk7 based CAK complex. TgCrk9 was found to functionally complement the role of its yeast counterpart Bur1 establishing its role as an important transcriptional kinase. In this study, we provide robust evidence that TgCrk9 is an important part of transcription machinery regulating gene expression in T. gondii.
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s): Mercedes Rubio, Jose Luis Maestro, Maria-Dolors Piulachs, Xavier Belles
Argonaute proteins are key in RNA silencing. In Drosophila melanogaster, the five proteins of the Argonaute family participate in the pathways and mechanisms mediated by three types of small RNAs: piRNAs, miRNAs, and siRNAs. Two Argonaute proteins, Argonaute 1 (Ago1) and Argonaute 2 (Ago2), are associated with miRNA and siRNA mechanisms, which are the most thoroughly studied. The available data points to a sorting specialization of Ago1 for miRNAs and Ago2 for siRNAs. However, this has been demonstrated only in D. melanogaster, one of the most modified insects, which emerged some 100 million years ago. Thus, an important question is whether this association of Ago1 with miRNAs and Ago2 with siRNAs occurs generally in insects, or was a specific innovation in higher flies.
We addressed this question by using RNAi approaches and studying Ago1 and Ago2 functions in the German cockroach, Blattella germanica, a much less modified insect that emerged some 320 million years ago.
The results showed that B. germanica does preferentially use Ago1 in the miRNA pathway, but can also use Ago2 in some cases. Conversely, Ago2 operates in the RNAi, in siRNA sorting, whereas Ago1 seems to have no relevant role in this process.
These basic associations are equivalent to those observed in D. melanogaster, implying that they have been evolutionary conserved from at least cockroach to flies, and possibly stem from the last common ancestor of extant insects.
Publication date: June 2018
Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6
Author(s): Quan Gan, Xinwei Zhang, Daobo Zhang, Liang Shi, Yue Zhou, Tongtong Sun, Song Jiang, Junshan Gao, Yan Meng
Sucrose is the most commonly transported sugar in plants and is easily assimilated by insects to fulfill the requirement of physiological metabolism. BmSuc1 is a novel animal β-fructofuranosidase (β-FFase, EC 3.2.1.26)-encoding gene that was firstly cloned and identified in silkworm, Bombyx mori. BmSUC1 was presumed to play an important role in the silkworm-mulberry enzymatic adaptation system by effectively hydrolyzing sucrose absorbed from mulberry leaves. However, this has not been proved with direct evidence thus far. In this study, we investigated sucrose hydrolysis activity in the larval midgut of B. mori by inhibition tests and found that sucrase activity mainly stemmed from β-FFase, not α-glucosidase. Next, we performed shRNA-mediated transgenic RNAi to analyze the growth characteristics of silkworm larvae and variations in glycometabolism in vivo in transgenic silkworms. The results showed that in the RNAi-BmSuc1 transgenic line, larval development was delayed, and their body size was markedly reduced. Finally, the activity of several disaccharidases alone in the midgut and the sugar distribution, total sugar and glycogen in the midgut, hemolymph and fat body were then determined and compared. Our results demonstrated that silencing BmSuc1 significantly reduced glucose and apparently activated maltase and trehalase in the midgut. Together with a clear decrease in both glycogen and trehalose in the fat body, we conclude that BmSUC1 acts as an essential sucrase by directly modulating the degree of sucrose hydrolysis in the silkworm larval midgut, and insufficient sugar storage in the fat body may be responsible for larval malnutrition and abnormal petite phenotypes.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Özge Çelik, Aybüke Ekşioğlu, Enes Yağız Akdaş
The main aim of the study is to identify the genes differentially, predominantly or specifically expressed in salt tolerant tobacco mutants, improved from Akhisar 97 and İzmir Özbaş varieties via mutation breeding, with respect to unstressed control plants. Seven tobacco mutants which have different salt tolerance capacities were evaluated by Gene Fishing analysis. Under stress conditions differentially expressed 100 reproducible bands were identified (74 of up-regulated and 20 of down-regulated while 6 were unknown). 75 of differentially expressed genes (DEGs) were successfully extracted from the gel and sequence analyses were performed. Functional annotation of the DEGs was performed against Blastn by interrogating their sequences. The 65 salt-regulated differentially expressed genes showed similarity with known genes, while 6 of DEGs didn't show any genetic similarities with known genes. DEGs were classified in eleven functional categories involving the abiotic stress response, biotic stress response, energy metabolism, cellular transport, catalitic activity, protein modification, amino acid metabolism and transcription factors. All the mutants were evaluated for their regulatory mechanisms against salt stress. The current data reveal that these six DEGs should be identified by next generation sequencing techniques and functional analysis should be design to understand the role of these six differentially expressed genes of tobacco mutants in further studies to improve new genetic resources.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Brian S. Grewe, Janet E. Richmond, David E. Featherstone
The Drosophila gene c12.2 was isolated in a screen examining mRNA binding proteins. Drosophila c12.2 is the mouse Vwa8 homolog. Various genome-wide associated studies have linked human Vwa8 to both neurological and oncological pathologies, which include autism, bipolar disorder, comorbid migraine, and acute myeloid leukemia, however, the function and role of the VWA8 protein remain poorly understood. To further analyze the Vwa8 gene in mouse, gene structure, protein homology modeling, and gene expression patterns were examined throughout mouse development. Our analyses indicate that the mouse Vwa8 gene produces two transcripts; the full-length Vwa8a is highly expressed relative to the truncated Vwa8b transcript across all developmental time points and tissues analyzed. Protein homology modeling indicates that VWA8a belongs to a novel protein superfamily containing both the midasin and cytoplasmic dynein 1 heavy chain 1 proteins. These data establish the development timeline and expression profile for both Vwa8a and Vwa8b, paving the way for future studies to determine the cellular role(s) of this highly conserved protein family.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Joanna K. Ledwon, Sergey Y. Turin, Arun K. Gosain, Jolanta M. Topczewska
Fibroblast growth factor (FGF) signaling is essential for many developmental processes and plays a pivotal role in skeletal homeostasis, regeneration and wound healing. FGF signals through one of five tyrosine kinase receptors: Fgfr1a, -1b, −2, −3, −4. To characterize the expression of zebrafish fgfr3 from the larval stage to adulthood, we used RNAscope in situ hybridization on paraffin sections of the zebrafish head. Our study revealed spatial and temporal distribution of fgfr3 transcript in chondrocytes of the head cartilages, osteoblasts involved in bone formation, ventricular zone of the brain, undifferentiated mesenchymal cells of the skin, and lens epithelium of the eye. In general, the expression pattern of zebrafish fgfr3 is similar to the expression observed in higher vertebrates.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Zimei Dong, Yibo Yang, Guangwen Chen, Dezeng Liu
The runt family genes play important roles in physiological processes in eukaryotic organisms by regulation of protein transcription, such as hematopoietic system, proliferation of gastric epithelial cells and neural development. However, it remains unclear about the specific functions of these genes. In this study, the full-length cDNA sequences of two runt genes are first cloned from Dugesia japonica, and their roles are investigated by WISH and RNAi. The results show that: (1) the Djrunts are conserved during evolution; (2) the Djrunts mRNA are widely expressed in intact and regenerative worms, and their expression levels are up-regulated significantly on day 1 after amputation; (3) loss of Djrunts function lead to lysis or regeneration failure in the intact and regenerating worms. Overall, the data suggests that Djrunts play important roles in regeneration and homeostatic maintenance in planarians.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Ryotaro Tsutsumi, Taro Chaya, Takahisa Furukawa
Cilia are essential for sensory and motile functions across species. In humans, ciliary dysfunction causes "ciliopathies", which show severe developmental abnormalities in various tissues. Several missense mutations in intestinal cell kinase (ICK) gene lead to endocrine-cerebro-osteodysplasia syndrome or short rib-polydactyly syndrome, lethal recessive developmental ciliopathies. We and others previously reported that Ick-deficient mice exhibit neonatal lethality with developmental defects. Mechanistically, Ick regulates intraflagellar transport and cilia length at ciliary tips. Although Ick plays important roles during mammalian development, roles of Ick at the adult stage are poorly understood. In the current study, we investigated the Ick gene expression in adult mouse tissues. RT-PCR analysis showed that Ick is ubiquitously expressed, with enrichment in the retina, brain, lung, intestine, and reproductive system. In the adult brain, we found that Ick expression is enriched in the walls of the lateral ventricle, in the rostral migratory stream of the olfactory bulb, and in the subgranular zone of the hippocampal dentate gyrus by in situ hybridization analysis. We also observed that Ick staining pattern is similar to pachytene spermatocyte to spermatid markers in the mature testis and to an intestinal stem cell marker in the adult small intestine. These results suggest that Ick is expressed in proliferating regions in the adult mouse brain, testis, and intestine.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Wei Wei, Jeremy Lotto, Pamela A. Hoodless
The Hippo signaling pathway regulates many cellular processes, but has been specifically associated with control organ size and tumor growth. Yes-associated protein 1 (YAP1) is a transcriptional cofactor, in the Hippo pathway, that regulates gene expression when localized in the nucleus. Elevated expression of YAP1 in adult mouse liver leads to hepatomegaly and can cause hepatocellular carcinoma; while the loss of function studies reveal its importance in regulating cholangiocyte development. Here, we report the expression of YAP1 in mouse embryonic and postnatal hepatic cells, using AFP-GFP transgenic mice to identify the hepatocyte lineage. At embryonic day (E) 8.5, YAP1 is highly expressed in the endoderm, but is not present in the nucleus. Between E9.5–12.5, hepatic cells display low levels of nuclear and non-nuclear YAP1. The nuclear expression of YAP1 is first detected in a small subset of hepatic cells starting at E13.5 when the hepatoblasts begin to differentiate into hepatocytes and cholangiocytes. At E18.5, nuclear YAP1 is nearly undetectable in hepatoblasts and hepatocytes, but enriched within the nuclei of cholangiocytes. These levels remain similar postnatally, consistent with the role of YAP1 in cholangiocyte specification and maintenance.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Rasoul Godini, Haider Yabr Lafta, Hossein Fallahi
Epigenetic modifications are involved in global reprogramming of the cell transcriptome. Therefore, synchronized major shifts in the expression of many genes could be achieved through epigenetic changes. The regulation of gene expression could be implemented by different epigenetic events including histone modifications, DNA methylation and chromatin remodelling. Interestingly, it has been documented that reprogramming of somatic cells to induced pluripotent stem (iPS) cells is also a typical example of epigenetic modifications. Additionally, epigenetic would determine the fates of almost all cells upon differentiation of stem cells into somatic cells. Currently, generation of iPS cells through epigenetic modifications is a routine laboratory practice. Despite all our knowledge, inconsistency in the results of reprogramming and differentiation of stem cells, highlight the need for more thorough investigation into the role of epigenetic modification in generation and maintenance of stem cells. Besides, subtle differences have been observed among different iPS cells and between iPS and ES cells. Although, a handful of detailed review regarding the status of epigenetics in stem cells has been published previously, in the current review, an abstracted and rather simplified view has been presented for those who want to gain a more general overview on this subject. However, almost all key references and ground breaking studies were included, which could be further explored to gain more in depth knowledge regarding this topic. The most dominant epigenetic changes have been presented followed by the impacts of such changes on the global gene expression. Epigenetic status in iPS and ES cells were compared. In addition to including the issues related to X-chromosome reactivation in the stem cells, we have also included loss of imprinting for some genes as a major drawback in generation of iPS cells. Finally, the overall impacts of epigenetic modifications on different aspects of stem cells has been discussed, including their use in cell therapy.
Publication date: September 2018
Source: Gene Expression Patterns, Volume 29
Author(s): Shuoqi Feng, Su Wang, Yashuo Wang, Qingyun Yang, Dejing Wang, Hongyan Li
Proteomic study has determined age-related changes in synthesis of carbonic anhydrase 2, myosin regulatory light chain 2 and selenium-binding protein 1 in muscle of post-menopausal women. However, little information is available regarding the expression and role of these proteins in early development and life span. In this study we showed that zebrafish ca2, myl2a, myl2b and selenbp1 were highly identical to their mammalian counterparts in primary and tertiary structures as well as genomic organization and syntenic map. They displayed distinct spatiotemporal expression patterns in embryos and larvae of zebrafish. Moreover, their transcription levels in the respective tissues were obviously remodeled in an age-dependent fashion, i.e. some mRNA levels were increased, while others remained unchanged or even decreased, suggesting that CA2, MYL2a, MYL2b and SELENBP1 can be used as aging biomarkers. Our study also lays a foundation for further illumination of the functions of these genes in early development and aging processes.
