A hominoid clavicle from the Mio-Pliocene of Sahabi, Libya

The first definitive hominoid from the Libyan Mio-Pliocene site of Sahabi is described. The specimen is a left clavicle, lacking a portion of the acromial end. In superior view it shows a marked sternal curvature, similar to homonids, but it also shows a curvature in the coronal plane, similar to the pongid condition. Muscle attachments for sternocleidomastoid, pectoralis major and the anterior portion of deltoid are preserved. The robust attachment for the latter suggests relative hypertrophy of this muscle. These considerations and certain morphological similarities to hominids do not suggest a functional reconstruction of locomotor behavior similar to Miocene dryopithecines. Nevertheless, more complete functional and taxonomic discussions must await further work at Sahabi.     

Spatio-temporal analysis of cetacean strandings and bycatch in a UK fisheries hotspot

Marine vertebrate strandings data can provide insights into the long-term dynamics of cetacean populations, and the threats they face. We investigate whether the spatio-temporal patterns of cetacean strandings around Cornwall, SW Britain, have changed in the past century. Analysis of strandings from 1911 to 2006 (n = 2,257) show that, since the mid-1970s, the relative frequency of strandings of common dolphins (Delphinus delphis), harbour porpoises (Phocoena phocoena) and pilot whales (Globicephala melas) has increased significantly. Seasonal peaks in strandings frequencies are apparent, between December and March for harbour porpoises and common dolphins, and between November and January for pilot whales. There were significant positive trends in the number of common dolphin and harbour porpoise strandings, as a proportion of total strandings, over time. Strandings of common dolphins, porpoises and all other species occur more frequently on the south coast of Cornwall. A total of 415 cetaceans were subject to full veterinary necropsy to determine cause of death, between 1990 and 2006, and 253 (61%) of these individuals were determined to have died due to bycatch in fishing gear. Analyses of industrialised fishing pressure in UK waters show the seas around Cornwall to be one of the most heavily fished areas of the UK. We suggest a number of factors that could be responsible for the recent increases in cetacean strandings in southwest UK waters in recent years, including survey effort, as well as abundance and range shifts that are potentially linked with climate change. Although detectable levels of bycatch rate have not increased over time, fisheries interactions are in significant part responsible for mortality patterns and are worthy of more detailed investigation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Comparative Approach Shows Differences in Patterns of Numt Insertion During Hominoid Evolution

Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes, although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole-genome sequences of single species or, more recently, from genomic comparisons across vast phylogenetic distances. Here we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 numts that have integrated into the chimpanzee nuclear genome since the human–chimp divergence, which is significantly greater than the 37 numts observed in humans. By comparing these closely related species, we accurately reconstructed the preintegration target site sequence and deduced nucleotide changes associated with numt integration. From >100 species-specific numts, we quantified the frequency of small insertions, deletions, duplications, and instances of microhomology. Most human and chimpanzee numt integrations were accompanied by microhomology and short indels of the kind typically observed in the nonhomologous end-joining pathway of DNA double-strand break repair. Human-specific numts have integrated into regions with a significant deficit of transposable elements; however, the same was not seen in chimpanzees. From a separate data set, we also found evidence for an apparent increase in the rate of numt insertions in the last common ancestor of humans and the great apes using a polymerase chain reaction–based screen. Last, phylogenetic analyses indicate that mitochondrial-numt alignments must be at least 500 bp, and preferably >1 kb in length, to accurately reconstruct hominoid phylogeny and recover the correct point of numt insertion. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Morphological study of the anthropoid thoracic cage: scaling of thoracic width and an analysis of rib curvature

While a relatively broad thorax and strongly curved ribs are widely regarded as common features of living hominoids, few studies have quantitatively examined these traits by methods other than calculating the chest index. The present study aims to quantify variations in thoracic cage morphology for living anthropoids. The odd-numbered ribs (first to eleventh) were articulated with the corresponding vertebrae and the cranial and lateral views subsequently photographed. Rib profiles were digitized in both views and line-fitted by a Bézier curve to create a three-dimensional morphological data set. When thoracic cage width was scaled against body mass, Hylobates (and possibly Pongo) plotted above non-hominoid anthropoids at almost all rib levels, while Pan did not differ from non-hominoid anthropoids. The overall pattern of the normalized thoracic width differed between Hylobates and other hominoids. In Hylobates, an upward convex curve was seen between the first and seventh ribs while a more linear pattern was observed in Pan and Pongo. This result quantitatively confirmed that the barrel-shaped thoracic cage in Hylobates can be distinguished from the funnel-shaped form in other hominoids. Conversely, all hominoids shared two distinct features in the upper half-thorax: (1) a pronounced dorsal protrusion of the proximal part of the rib in accordance with ventral displacement of the thoracic spine and (2) a relatively medially projecting sternal end. Although these features are likely to provide some mechanical advantage in orthograde and/or suspensory positional behaviors, they were barely present in the suspensory Ateles. An erratum to this article can be found at     

A set of polymorphic dinucleotide and tetranucleotide microsatellite markers for the Indo-Pacific humpback dolphin (Sousa chinensis) and cross-amplification in other cetacean species

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as ‘data deficiency’ in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species’ conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10–13 loci have successful cross-amplifications.     

Calcium,phosphorus, calcium-phosphorus ratio in rib bone of healthy humans

Calcium and phosphorus concentrations as well as the Ca/P ratio were estimated in intact rib bone samples from healthy humans, 37 women and 45 men, aged 15–55 yr. For Ca and P concentration measurements, instrumental neutron activation analysis was used. The mean values (mean±SD) for the investigated parameters were 19.3±4.5% of dry bone weight, 8.42±2.14% of dry bone weight, and a ratio of 2.33±0.34, respectively. Statistically significant differences for the above parameters were not observed to be related either to age or sex. The mean values for Ca, P, and the Ca/P ratio were within a very wide range of published data and close to their medians. The individual variation for the Ca/P ratio in rib bone from healthy humans was lower than those for Ca and P taken separately. An indication is that the specificity of the Ca/P ratio improves upon that for Ca and P concentrations and may be more reliable in the diagnosis of bone disorders.     

Early-replicating DNA from mosquito cells is associated with a distinct EcoRI fragment

In an effort to define an origin of bi-directional DNA replication (OBR) in mosquito genomic DNA, we applied methods that take advantage of characteristic features of single-stranded DNA to methotrexate-resistant Aedes albopictus cells. The Mtx-5011-256 cells contained approximately 1000 copies of a 200 kb amplicon containing the dihydrofolate reductase locus, which likely contained one or more replication origins. When Mtx-5011-256 cells were synchronized by treatment with hydroxyurea, released into the S phase of the cell cycle, and labeled in vivo with tritiated DNA precursors, a 1.9 kb EcoRI fragment was preferentially labeled in EcoRI-digested genomic DNA. Similarly, we detected a 1.9 kb EcoRI fragment in DNA from wild type cells after cell cycle synchronization and in vivo labeling. In a complementary method, unlabeled single-stranded DNA was isolated from Mtx-5011-256 cells, labeled in vitro, and hybridized to EcoRI-digested genomic DNA from mosquito cells. The labeled probe hybridized preferentially to a 1.9 kb fragment. Finally, a 1.9 kb EcoRI fragment was detected when nascent DNA was recovered from unsynchronized cells, made double-stranded by in vitro labeling, and digested with EcoRI. Taken together, these results suggest that in Aedes albopictus mosquito cells, many replication origins used at different times during S are flanked by EcoRI sites that define a 1.9 kb fragment, which has become more abundant in Mtx-5011-256 cells because it occurs in the dhfr amplicon. Tentative mapping of this origin to amplicon DNA remains ambiguous, further suggesting that a repeated sequence element occurs at or near the origin of replication.     

Dentognathic remains of an Afropithecus individual from Kalodirr,Kenya

We describe here the well-preserved dentognathic remains of an Afropithecus individual from the early Miocene site of Kalodirr in northern Kenya. The specimen includes a nearly complete dentition in which most of the crowns are undamaged and unworn. The new information gleaned from this specimen adds to our knowledge of this genus in several ways. Afropithecus exhibits an atypical pattern of canine dimorphism, and is probably more easily sexed by the pattern of variation in its upper premolars. Both phenomena are likely related to the modification of its antemolar dentition for the purpose of sclerocarp harvesting. The new fossils clarify the role in this adaptation of the premolars, which appear specialized for initiating and propagating cracks in large food items bearing protective coats. Comparison with other Miocene apes suggests that the closest known relative of Afropithecus is Nacholapithecus, to which Equatorius is more distantly related. Morotopithecus shares some primitive traits with Afropithecus, but lacks the derived features shared by the latter and Nacholapithecus.     

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in hominoidea

Summary A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly.The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.     

A new species of Propliopithecus from the Fayum, Egypt

Propliopithecus ankeli is described as a new species of hominoid from the early Oligocene of Egypt. The new species occurs at a stratigraphic level 80 m below quarries yielding P. chirobates and Aegyptopithecus zeuxis. P. ankeli differs from other species of the genus in its large size, relatively robust canines, larger and proportionally broader premolars, and M1 that has as great or greater mesiodistal length than M2. Thus, P. ankeli is characterized by increased relative size and robustness of the antemolar dentition, which contrasts with the pattern observed in the Fayum's other large hominoid, A. zeuxis. P. ankeli probably represents a lineage not ancestral to other Fayum hominoids. Discovery of this new species emphasizes the diversity of anthropoid primates that had already evolved by the early Oligocene.     

Evidence that the chromogranin B fragment 368-417 extracted from a pheochromocytoma is phosphorylated

A rabbit antiserum was raised against a synthetic peptide corresponding to residues 403 to 417 of human chromogranin B. This peptide was chosen to match the potential C-terminal end of a putative proteolytic fragment of the protein located between dibasic doublets in positions 366-367 and in positions 418-419 of the precursor. A radioimmunoassay based on this antiserum was developed and used to detect the protein or a fragment thereof in a pheochromocytoma tumor extract. One fragment was purified to homogeneity by successive reverse-phase HPLC chromatographies. The N-terminal sequence established by automated Edman degradation, was N-Y-P-S-L-E-L-D-K-M-A-H-G-Y-G-E-E-S-E-E-E-R corresponding to the 368-389 sequence of human chromogranin B. Taking into account the specificity of the antiserum used for peptide identification and alignment with the precursor sequence, we deduced that the purified peptide was chromogranin B (368-417) and represented a new peptide generated by limited proteolysis of chromogranin B. Combining electrospray mass-spectrometry and enzymatic dephosphorylation, we demonstrated that this peptide was phosphorylated.     

Lipokeratinocytes of the epidermis of a cetacean (Phocena phocena)

Summary Biochemical and ultrastructural analysis of epidermis from the porpoise, Phocena phocena, revealed certain similarities and differences between cetaceans and terrestrial mammals. The predominant cell of cetacean epidermis, not found in normal terrestrial mammals, is a lipoker-atinocyte, which elaborates not only keratin filaments, but also two types of lipid organelles: first, lamellar bodies, morphologically identical to those of terrestrial mammals, are elaborated in great abundance in all suprabasal epidermal layers, forming intercellular lipid bilayers in the stratum corneum interstices: and second, non-membrane-bounded droplets appear and persist in all epidermal layers. Although the porpoise lipokeratinocyte morpologically resembles the sebokeratocyte of avians in certain respects, nonmembrane-bounded lipid droplets are not released into the intercorneocyte space as they are in avian stratum corneum. Whereas phospholipid/neutral lipid gradients are similar in porpoise and terrestrial mammals, PAS-positive glycoconjugates, specifically glycosphingolipids, are retained in porpoise stratum corneum, but lost from these layers in terrestrials. The novel, non-polar acylglucosyl-ceramides, which also are lost during cornification in terrestrial mammals, are retained in porpoise stratum corneum. The lipid components of porpoise lipokeratinocytes appear to subserve not only barrier function in a hypertonic milieu, but also underlie the unique buoyancy, streamlining, insulatory, and caloric properties exhibited as adaptations to the cetacean habitat.     

Isolation of a raw starch-binding fragment from barley alpha-amylase

Barley -amylase was purified by ammonium sulfate fraction, ion-exchange, ultrafiltration, and gel filtration to homogeneity. The purified enzyme was partially digested with trypsin, and the reaction mixture was applied to a cyclohepta-amylose epoxy Sepharose 6B column. Bound fragments were eluted by free cyclohepta-amylose, lyophilized, and separated on Tricine gels. Four fragments were shown to interact with -cyclodextrin. The fragment that could be identified on the gel with the lowest molecular weight (11 kDa) was electroblotted onto PVDF membrane for sequencing. The N-terminal sequence of this fragment was determined with the N-terminal amino acid corresponding to Ala283 in the whole protein. The trypsin cleavage was at Lys282/Ala283 and the C-terminal cleavage occurred at Lys354/Ile355 to give a fragment size of 11 kDa as estimated by SDS-PAGE. The fragment would be located at the C-terminal region, forming a majority of the antiparallel -sheets in domain C and the ₇-and ₈-helices of the (/)₈ domain.     

Characterization of a chondrocyte primary culture from rib cartilage of the rat

In order to standardize and to characterize a chondrocyte primary culture, cells from rat rib resting cartilage were used. High yield (0.99 +/- 0.18 x 10(6) cells/rat) and viability (91.76%) of costal cartilage cells was reached by enzymatic digestion with collagenase. The cells were cultivated in Dulbecco's medium (DME) supplemented with 10%. Heat inactivated newborn calf serum, at 37 degrees under humidified atmosphere of 5% CO2 in air. Two or three days after plating, the cells were attached to the surface of tissue culture weel, and began dividing. Adhesion was independent of plating density. The doubling time of cell population was found to be 23.19 hours. The cells became a monolayer and required easy maintenance. The results support the contention that rat costal cartilage is a good source of chondrocytes for primary culture cells experiments.     

PI-specific phospholipase C "alpha" from sheep seminal vesicles is a proteolytic fragment of PI-PLC delta.

Phosphatidylinositide-specific phospholipase C enzymes (PLCs) catalyze the conversion of the phosphoinositides to biologically important signal transducing molecules. These enzymes may be grouped into "families" which share similar structures and modes of regulation. The existence of a structurally distinct family of PLC termed "alpha" has been recently called into question. In the current paper we show by immunoblotting experiments that PLC "alpha" from sheep seminal vesicles is recognized by monoclonal antibodies raised against the delta 1 isoform of bovine brain PLC, and appears to be derived from a higher molecular weight band at 85 kDa. We also show that antibodies raised against PLC alpha efficiently immunoprecipitate the 85-kDa PLC delta 1 isoform from bovine brain and Chinese hamster lung fibroblasts. These data provide strong evidence that the PLC alpha from sheep seminal vesicles is a proteolytic fragment of PLC delta 1. Thus, there is still no conclusive evidence for a separate "alpha" class of PLC.     

Functional and morphological affinities of the subadult hand (O.H. 7) from Olduvai Gorge.

Study of the O.H. 7 hand was based primarily on morphological comparisons with a large series of hand skeletons of extant hominoid primates. Most of the hand elements are fragmentary or have missing epiphyses and only comparisons based on qualitative morphological observations are possible. The distal phalanges are complete, however, and were analyzed metrically utilizing univariate and multivariate statistical techniques. To compensate for size differences among the Hominoidea a number of size adjustments were employed. None of the adjustments were totally satisfactory from theoretical and practical standpoints and none completely eliminated the influence of size. There is no entirely satisfactory procedure to eliminate size and it is advisable to use several techniques that are not closely related, to compare the results and interpret them with caution. In certain features the wrist and fingers resemble those of African apes; in others they are more like modern human hands; in still others they are unique. The scaphoid and the proximal articular surface of the trapezium retain ape-like features, as do the proximal and middle phalanges. The pollical carpometacarpal joint and the distal phalanges are closer in morphology to those of modern humans. The scaphoid, proximal phalanges and middle phalanges of rays II-V indicate a hand capable of a strong power grip. A number of features of the thumb and the distal phalanges suggest that the O.H. 7 individual was capable of more precise manipulation that extant apes. FLK NN-A, a first distal phalanx, does not closely resemble the first distal phalanx of any of the living Hominoidea. Multivariate distance analysis indicates, however, that it is closest in overall morphology to the pollical distal phalanx of modern humans. In some features not included in the metric analysis, FLK NN-A also resembles the hallucial distal phalanx of modern humans.     

Podoplanin is expressed by a sub-population of human foetal rib and knee joint rudiment chondrocytes

The aim of this study was to determine if podoplanin was expressed by rudiment chondrocytes in human foetal cartilages. Podoplanin was immunolocalised in first trimester human foetal rib and knee joint rudiments to a sub-population of chondrocytes deep in the rib rudiments, tibial and femoral growth plates and cells associated with the cartilage canals of the foetal knee joint rudiments. Lymphatic vessels in the loose stromal tissues surrounding the developing rudiments were also demonstrated on the same histology slides using antipodoplanin (MAb D2-40) and anti-LYVE-1 and differentiated from CD-31 positive blood vessels confirming the discriminative capability of the antibody preparations used. The D2-40 positive rib and knee rudiment chondrocytes were not stained with antibodies to LYVE-1, CD-31 or CD-34 however perlecan was a prominent pericellular proteoglycan around these cells confirming their chondrogenic phenotype. Discernable differences were evident between the surface and deep rudiment chondrocytes in terms of their antigen reactivities detected with MAb D2-40 or antiperlecan antibodies. Binding of the cytoplasmic tail of PDPN to the ERM proteins ezrin, radixin and moeisin may result in changes in cytoskeletal organisation which alter the phenotype of this central population of rudiment cells. This may contribute to morphological changes in the rudiment cartilages which lead to establishment of the primary ossification centres and is consistent with their roles as transient developmental scaffolds during tissue development.