Production of HIV-1 Vpu with pYEULCBX,a convenient vector for the production of non-fused proteins in yeast

Summary Site directed mutagenesis was employed to modify a vector previously constructed for the convenient, copper-inducible production of fusion proteins in the yeastSaccharomyces cerevisiae. The resulting vector, pYEULCBX, remains versatile and now permits nonfused proteins to be produced. Thevpu gene from HIV-1 was expressed as an example.     

Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, <Emphasis Type="Italic">Rallus aquaticus</Emphasis> and <Emphasis Type="Italic">R. indicus</Emphasis>

Background  

Water Rails (Rallus aquaticus) inhabit fragmented freshwater wetlands across their Palearctic distribution. Disjunct populations are now thought to be morphologically similar over their vast geographic range, though four subspecies had been recognized previously. The fossil record suggests that Water Rails (R. aquaticus) were already spread across the Palearctic by the Pleistocene ~2 million years ago, and the oldest fossil remains thought to be closely related to the common ancestor of water rails date from the Pliocene.     

Agrobacterium as a tool for gene transfer in woody species: The state of the art and practical perspectives. A review

Abstract

The Agrobacterium-mediated ability to transfer genes into organisms without sexual crossing provides breeders with new opportunities to improve the efficiency of plant production. Gene transfer offers advantages over classical genetic manipulation since plants are improved without disruption of the integrity of their genomes. Several useful genes isolated from microrganisms and affecting pest resistance, rooting ability, hormonal metabolism etc., are now available. These genes can be easily cloned into suitable Ti and Ri derived plasmid vectors and transferred into woody species. The scarce ability of most fruit trees to regenerate the whole plant from in vitro-cultured cells remains the main obstacle to a wider use of gene transfer technology.     

Micromammals from the type site of Broken Hill Man (Homo rhodesiensis) near Kabwe,Zambia: a historical note

Abstract

The presence of large numbers of micromammalian remains near the Homo rhodesiensis (now H. heidelbergensis or H. sapiens) type cranium from the Broken Hill Mine near Kabwe was noted when it was discovered. Most of the remains seem to have been lost but a small sample was preserved in the palaeontology collections at the Natural History Museum, London. Over the years, this sample received preliminary inspections that resulted in various published and unpublished reports or identifications, copies of which were kept with the material. The unpublished reports are reproduced to place them on record and to complement the more complete annotated systematic list for the site now given. The present paper collates previous identifications, adds some previously unrecorded taxa and updates the taxonomy to conform to current thinking. The partial nature of the sample prevents a detailed interpretation of environmental conditions at the time of accumulation and there remains no direct dating of the site. However, the micromammals suggest that the environment at the time of deposition was much as it would have been before mining and other human activities altered the vegetation, which may imply interglacial conditions.     

A SPALACOLESTINE SPALACOTHERIID (MAMMALIA,TRECHNOTHERIA) FROM THE EARLY CRETACEOUS (BARREMIAN) OF SOUTHERN ENGLAND AND ITS BEARING ON SPALACOTHERIID EVOLUTION

Abstract: Bulk screening of Early Cretaceous (Barremian) Wealden Group strata of the Wessex Formation exposed on the south‐west and south‐east coasts of the Isle of Wight, southern England, has resulted in the recovery of fragmentary remains pertaining to a new spalacolestine spalacotheriid mammal, Yaverlestes gassoni gen. et sp. nov. These represent the first European record of the Spalacolestinae. The remains comprise a dentulous incomplete dentary and isolated upper and lower molariforms, the former representing the most substantial mammal remains yet recovered from the Wealden Group. Hitherto, six species of spalacotheriid mammal were known from the Lower Cretaceous of Europe. All are referred to the genus Spalacotherium but in the case of taxa diagnosed on the basis of isolated lower teeth and other specimens where the post‐canine dentition is incompletely known, it is now evident that these referrals should be treated with caution. Furthermore, the new Wessex Formation spalacotheriid and recently described spalacotheriids from the ?Barremian of Japan, and the Barremian and Aptian of China exhibit combinations of characters that suggest that spalacotheriids were more diverse and that their evolution was more complex than previously recognized. The systematic position of an isolated tooth from the basal Cretaceous Lourinhã Formation of Portugal is discussed and the tooth reassigned to the Spalacotheriidae. Together with the new Wessex Formation taxon, eight species are now known from the Lower Cretaceous of Europe. The discovery of a spalacolestine in the Barremian Wessex Formation supports the concept of faunal interchange between Europe, Asia and North America during the Early Cretaceous. It also supports derivation of North American spalacotheriids from a European or Eurasian ancestor.     

Review and Detailed Description of Sauropod-Dominated Trackways from the Upper Cretaceous Jiangdihe Formation of Yunnan,China

Type specimens of the sauropod ichnotaxon Chuxiongpus changlingensis, which was later reassigned to Brontopodus changlingensis, as well as the theropod ichnotaxon Yunnanpus huangcaoensis, both from the Cretaceous Jiangdihe Formation of Yunnan Province, are redescribed in order to document their morphological features. Both, but particularly Y. huangcaoensis, which is considered now a nomen dubium, were originally based on poorly preserved material. Nevertheless, the specimens document a saurischian dominated biota that existed during the deposition of the Jiangdihe Formation from which no skeletal remains are known. B. changlingensis trackways were left by small sauropods that show consistent partial or complete overprint of the manus by the pes. This pattern makes it difficult to calculate manus length, and heteropody can be only estimated.     

Shotgun microbial profiling of fossil remains

Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next‐generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200‐ to 13 000‐year‐old horse bones collected from northern Siberia. We use a robust, taxonomy‐based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site‐specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.     

Giving the early fossil record of sponges a squeeze

Twenty candidate fossils with claim to be the oldest representative of the Phylum Porifera have been re‐analysed. Three criteria are used to assess each candidate: (i) the diagnostic criteria needed to categorize sponges in the fossil record; (ii) the presence, or absence, of such diagnostic features in the putative poriferan fossils; and (iii) the age constraints for the candidate fossils. All three criteria are critical to the correct interpretation of any fossil and its placement within an evolutionary context. Our analysis shows that no Precambrian fossil candidate yet satisfies all three of these criteria to be a reliable sponge fossil. The oldest widely accepted candidate, Mongolian silica hexacts from c. 545 million years ago (Ma), are here shown to be cruciform arsenopyrite crystals. The oldest reliable sponge remains are siliceous spicules from the basal Cambrian (Protohertzina anabarica Zone) Soltanieh Formation, Iran, which are described and analysed here in detail for the first time. Extensive archaeocyathan sponge reefs emerge and radiate as late as the middle of the Fortunian Stage of the Cambrian and demonstrate a gradual assembly of their skeletal structure through this time coincident with the evolution of other metazoan groups. Since the Porifera are basal in the Metazoa, their presence within the late Proterozoic has been widely anticipated. Molecular clock calibration for the earliest Porifera and Metazoa should now be based on the Iranian hexactinellid material dated to c. 535 Ma. The earliest convincing fossil sponge remains appeared at around the time of the Precambrian‐Cambrian boundary, associated with the great radiation events of that interval.     

Restriction enzyme cleavage of DNA resulting from gently lysed Escherichia coli.

Summary When E. coli or infected E. coli are gently lysed the DNA is released as a very fast sedimenting species that is presumably bound to membrane material. If this complex is now subjected to restriction enzyme cleavage, only a minor fraction of the fast sedimenting DNA remains and this is found, after purification, to be enriched for branched molecules.     

Fossilized fungi as evidence of continental drift

According to Wegener (1912), about 200 million years ago the once unitary land mass that he named Pangea, became fragmented into the several continents. Subsequently these continents have continued to drift.The present account deals with the occurrence of fossilized fungal remains in Chattanooga shale and such fossils are interpreted as evidence of the occurrence of continental drift. Chattanooga shale consists of two materials, shale and the highly carbonized remains of a floating, aquatic, green plant, Conodontophyta chattanoogae, that now is an extinct, nonpetrified fossil. The remains of this fossil became compressed between layers of finegrained shale. When a piece of shale is struck with a hammer it breaks apart at the bedding planes and thus exposes fossilized Conodontophyta tissues. By examination with a dissecting microscope, the fungal remains may be seen to occur on the Conodontophyta tissues. Fragments of the carbonized tissues are filled with hyphae and with dark fungal nodules. When these nodules are removed with a dissecting needle tipped with Canada balsam and are mounted on a microscope slide, and pressure is applied to the coverglass, the nodules break apart. The parts consist of hyphae, spores, and ascocarps. These fungi are like some of the species presently in soils of the several continents. Fossil fungi as well as present-day widely distributed ones therefore may be regarded plausibly as evidence of the occurrence of continental drift.     

The oldest durophagous teleosauroid (Crocodylomorpha,Thalattosuchia) from the lower Bathonian of central High Atlas,Morocco

Marine crocodylomorphs were particularly abundant in Europe during the Middle Jurassic, but were very scarce in Africa. New finds of thalattosuchian cranial remains in Morocco suggest that this scarcity is probably related to poor sampling rather than original diversity. These remains pertain to the coastal thalattosuchians, the teleosauroids, and particularly to the clade grouping the blunt‐toothed ‘Steneosaurus’ obtusidens and the genus Machimosaurus. A new tribe is erected grouping these two taxa: Machimosaurini. Until now the machimosaurins have been known from the middle Callovian. The new material extends the presence of this group further back to the lower Bathonian, nearly 5 myr earlier. The machimosaurins are the only teleosauroid group that has been recently reviewed, and the difference between the revised diversity provided herein and that previously reported is large. A review of other teleosauroids and clear establishment of their phylogenetic relationships are also likely to have considerable impact on their observed diversity. So, until a complete review of the teleosauroids is carried out, the results of crocodylomorph diversity analyses should be treated with caution.     

Die Entwirrung desBotrytella(Sorocarpus)-Komplexes (Ectocarpaceae,Phaeophyta)

Sorocarpus Pringsh. is a later synonym forBotrytella Bory. Four species of the genus are known from northern European coasts. Three of them are found at Helgoland (North Sea), type locality of bothBotrytella uvaeformis (Pringsh.) andB. reinboldii (Reinke). A third species, most frequently seen, still remains unnamed. Plants of similar habit, however, have been described from Japan. The type species for the genus,Botrytella micromora Bory, was originally published asEctocarpus siliculosus β.uvaeformis by Lyngbye. A sample from Danish waters proved to be identical with it. In a previous paper (Kornmann & Sahling, 1984), the life history of two species was studied and the investigation is now extended to include the other two, demonstrating the conformity of the four species with the genus characters as to morphological and developmental features.      

Multipotent progenitor cells in the adult dentate gyrus

Neurogenesis persists in the adult dentate gyrus of rodents throughout the life of the organism. The factors regulating proliferation, survival, migration, and differentiation of neuronal progenitors are now being elucidated. Cells from the adult hippocampus can be propagated, cloned in vitro, and induced to differentiate into neurons and glial cells. Cells cultured from the adult rodent hippocampus can be genetically marked and transplanted back to the adult brain, where they survive and differentiate into mature neurons and glial cells. Although multipotent stem cells exist in the adult rodent dentate gyrus, their biological significance remains elusive. © 1998 John Wiley & Sons, Inc. J Neurobiol 36: 249–266, 1998.     

Footprints of Giant Birds from the Upper Eocene of the Paris Basin: An Ichnological Enigma

In 1859 the French geologist Jules Desnoyers reported the discovery of vertebrate footprints in the Late Eocene gypsum of the Paris region. Although they attracted some attention at the time, those footprints were never illustrated or described in detail, and the present whereabouts of the specimens seem to be unknown. Several types of footprints were referable to animals known by skeletal elements from the gypsum, but some were not. Among the latter were tridactyl footprints of very large birds, which Desnoyers tentatively attributed to the giant ground bird Gastornis, which had been discovered in the Lower Eocene of the Paris region a few years earlier. Gastornithids are now known from the Paleocene to the Middle Eocene, but no skeletal remains of giant birds have yet been found in the Upper Eocene of Europe. The tracks of giant birds from the gypsum of the Paris region are thus an example of fossil footprints without known osteological counterparts, and the identity of the trackmakers remains an enigma.     

Sangiran 5,(“Pithecanthropus dubius”), homo erectus, “Meganthropus,” orPongo?

There are now eleven known mandibular remains from the Lower and Middle Pleistocene of Java, all but one being from the Sangiran site. All of these have been assigned toHomo erectus by most workers, while others have suggested as many as four different hominoid taxa. The author finds that the jaws cannot be a homogeneous sample. Morphologically, they are a mixture of undoubtedH. erectus, “H. meganthropus,” and possibly a pongid. If the jaws are allH. erectus then they have a sexual dimorphism exceeding that of modern gorillas. The case of“Pithecanthropus dubius” (Sangiran 5) is even less certain; even its hominid status is disputed. If it is indeedHomo it must be placed with the other“H. meganthropus” specimens. Its size and morphology are well beyond the known range anyH. erectus.     

Callistophytalean pteridosperms from Permian aged floras of China

Abstract: Recent investigations into Permian aged floras from China have highlighted the widespread occurrence of callistophytalean pteridosperms that challenge previous understanding of their spatial and temporal distribution and diversity. In China, the group spans the Permian period and constitutes a distinctive but rare component in many peat‐forming environments. The stratigraphically earliest callistophytalean occurs in the Asselian‐Sakmarian stages with fossils from the Taiyuan Formation of northern China including ovules of Callospermarion undulatum in coal ball assemblages, and ovulate fronds of Norinosperma shanxiensis and synangiate fronds of Norinotheca shanxiensis in adpression assemblages. More abundant in the fossil records are adpression remains from the Roadian‐Wordian stages with the Lower Shihhotse Formation preserving abundant vegetative and ovulate remains of Emplectopteris triangularis that is now considered to represent a callistophytalean. The youngest callistophytalean recognised is from the Wuchaipingian‐Changhsingian stages with the Xuanwei Formation of southern China containing a single stem of Callistophyton boyssetii that provides indisputable evidence of the group in the lead up to the end‐Permian mass extinction. These accounts are augmented by analysis of pollen records that demonstrate the callistophytalean pollen genus Vesicaspora to be widespread through palynological assemblages from the Permian period in both North and South China, including the Upper Shihhotse Formation, Shihchienfeng Group, Xuanwei Formation, and possibly also in the mid‐Pennsylvanian Benxi Formation. Although macrofossil specimens are uncommon elements in the assemblages that contain them, they demonstrate the continuity of callistophytalean pteridosperms from the Pennsylvanian sub‐period into the early Guadalupian epoch of the Permian in North China and into the Lopingian epoch of the Permian in South China. Of the species present, both Callistophyton boyssetii and Callospermarion undulatum are known from the Pennsylvanian–earliest Permian age floras of Euramerica, whereas Norinosperma, Norinotheca and Emplectopteris appear to represent endemic Cathaysian elements. Results imply that callistophytalean pteridosperms can no longer be excluded from theories of post‐Carboniferous plant evolution and floristics, appearing to have played an important role in both Permian and Carboniferous aged plant communities. The presence of Vesicaspora in several formations from which macro‐remains have not been identified is a hopeful indicator that further callistophytalean pteridosperms are yet to be found.     

Phylogenetic reassessment of gorals with new evidence from northern Myanmar reveals five distinct species

Researchers have recognised one to seven species of goral (Naemorhedus spp., Caprinae, Bovidae). We compared all available whole mitogenomic sequences, including eight new ones from northern Myanmar, and now recognise five distinct species. Naemorhedus caudatus remains a valid species. Naemorhedus griseus is a synonym of Naemorhedus goral. Naemorhedus evansi is a valid species, with a geographic range that extends northwards into southwestern China. Naemorhedus cranbrooki and Naemorhedus baileyi are distinct species, not synonyms. Molecular divergence analyses suggest that goral speciation was closely related to the rapid uplift of the Qinghai-Tibetan Plateau and Hengduan Mountains from the early Pliocene to the Pleistocene.     

Evidence for the teleosaurid crocodylomorph genus Machimosaurus in the Kimmeridge Clay Formation (Late Jurassic) of England

We report the only definite specimen of the teleosaurid crocodylomorph genus Machimosaurus from the Kimmeridge Clay Formation of England. This specimen (an isolated tooth) is now the only evidence of Machimosaurus in the Kimmeridge Clay Formation because a large skull and mandible, previously considered to be of Machimosaurus mosae, was recently shown to pertain to a metriorhynchid crocodylomorph. The tooth described herein was originally figured in 1884 as a tooth crown from a metriorhynchid crocodylomorph. However, its conical shape, blunt apex and distinctive enamel ornamentation are characteristic of the teleosaurid genus Machimosaurus. That Machimosaurus, and teleosaurids in general, were so rare in the Kimmeridge Clay Formation suggests that these marine crocodylomorphs did not commonly use this seaway. Their rarity is in contrast to contemporaneous deposits from continental Europe where teleosaurid remains, including Machimosaurus, are far more common. These continental deposits were deposited in shallow-marine/brackish ecosystems, suggesting that teleosaurids were largely restricted to coastal marine environments.     

Archaeobotanical analysis of some early Neolithic settlements in the Kujawy region, central Poland, with potential plant gathering activities emphasised

Neolithic settlements in the Kujawy region of central Poland are represented by seven archaeological sites which have botanical material archaeologically dated to the Linear Pottery culture (LBK) (ca. 5400-5000 cal. B.C.) and the Lengyel culture (ca. 4400-4000 cal. B.C.). The composition of plant remains suggests that Stipa pennata s.l. played a certain role in the economy of the Neolithic settlers. The presence of this xerothermic grass is best explained by local gathering rather than distant transport or coming into the sediment by chance. The finding of Hierochlo? cf. australis grains represents the first identification of this plant in archaeobotanical material from Poland. This, now rare, plant contains coumarin and for this reason could have been useful in prehistory. Other plants such as Bromus spp., Chenopodium album type, Fallopia convolvulus and Galium spp. were found in large quantities, and although common weeds now, they could also have been collected by the Neolithic settlers. Plants such as Corylus avellana and Vaccinium vitis-idaea that are typically considered to be collected as foods are present in the studied material but in very small quantities. Received September 17, 2001 / Accepted March 13, 2002     

Avian remains from the Upper Pleistocene (MIS3) site of Aguilón P-7, south of the Ebro River,Spain

Aves are represented by abundant fossil remains in Quaternary sites. Birds are well adapted to the environment they inhabit, so they make very good paleoenvironmental indicators for Quaternary sites. Here we analyse the avian remains from the Late Pleistocene (probably MIS3) site of Aguilón P-7 (AGP-7). The Pleistocene sediments fill up a shallow cave, which is located in the Zaragozan part of the Iberian Range, 55 km south of the city of Zaragoza. We have for the first time provided a taxonomic and taphonomic study of the avian assemblage of AGP-7, as well as a preliminary paleoenvironmental analysis based on these data. Nine avian taxa have been identified: Galliformes indet., Lagopus sp., Aquila chrysaetos, Gyps fulvus, Passeridae indet., Anthus sp., Prunella modularis,Sturnus cf. unicolor and Corvus monedula. The taphonomic analysis did not provide conclusive information. However, it suggests an accumulation of uneaten food remains by diurnal birds of prey. The identified taxa currently inhabit the Iberian Peninsula, populating woodland environments with rocky areas. They are found in areas with an oceanic climate, in contrast to the Mediterranean climate that now prevails in Aguilón.