Darting Primates: Steps Toward Procedural and Reporting Standards

Darting, a common method of capturing wild primates, poses risks to the individuals that must be appropriately minimized. A recent article in the International Journal of Primatology by Cunningham et al. (International Journal of Primatology, 36(5), 894–915, 2015) presented a literature review of the reporting of darting procedures in primatology and anonymously surveyed primatologists on darting methods and their effects, to report general trends in the field. We quantitatively reexamined 29 articles described by the authors as having information on fatalities and/or injuries. We think that the various body masses of primates (1 kg–150 kg), along with their locations and habitat types, and the degree of experience of the darting team, should be considered when estimating mortality and injury rates, and thus preclude the computation of an average mortality value across taxa. Nevertheless, we computed an average (mean) for comparison with the previous analyses. Our mean estimated mortality rate was 2.5% and the mean estimated injury risk was 1.5% (N = 21 articles). Thus, our estimated mortality rate is smaller than the combined mortality and injury rate of 5% reported by Cunningham et al. (International Journal of Primatology, 36(5), 894–915, 2015) and smaller than the mortality rates of medium-sized terrestrial mammals they used for comparison. Our study strongly suggests the critical need for more data to be analyzed in a standardized fashion.     

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Background

The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, Science, 306, 630–631, 2004), by extensively citing the study of Tan et al. (Nucleic Acids Res., 31, 5676–5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology.

Results

We reanalyzed Tan's dataset and found that the intra-platform consistency was low, indicating a problem in experimental procedures from which the dataset was generated. Furthermore, by using three gene selection methods (i.e., p-value ranking, fold-change ranking, and Significance Analysis of Microarrays (SAM)) on the same dataset we found that p-value ranking (the method emphasized by Tan et al.) results in much lower cross-platform concordance compared to fold-change ranking or SAM. Therefore, the low cross-platform concordance reported in Tan's study appears to be mainly due to a combination of low intra-platform consistency and a poor choice of data analysis procedures, instead of inherent technical differences among different platforms, as suggested by Tan et al. and Marshall.

Conclusion

Our results illustrate the importance of establishing calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms and the proficiency of individual laboratories as well as the merits of various data analysis procedures. Thus, we are progressively coordinating the MAQC project, a community-wide effort for microarray quality control.

     

Serology and Genetics of a New Blood Type Bm

TYPE Am, a variation of the A blood type, was discovered by Weiner et al.¹ and further studied by Salmon et al.² and HrubiSko et al.^3,4. Ikemoto et al.⁶ conducted family surveys on type Bm ⁵ in Japanese subjects. Although there have been genetic surveys and studies of the antigenicity of red cells, nobody has yet quantified the immune globulins in serum, the effect of the B and O decomposing enzymes on the Bm red cells, the genetic polymorphism of the plasma or the antigenicity of hairs and cells in the oral mucosa. Recently we surveyed a family, F, of type Bm which included monozygotic twins. We report now further surveys on some of the members of that family and discuss their antigenic relationships and Furuhata's⁷ triple allelomorph theory, that blood type antibodies are genetically determined.     

Transneuronal Degeneration as Basic Mechanism of Muscular Atrophy of Central Origin (Reply)

WE wish to report some findings which are relevant to the recent work of McComas et al.¹. Although our EMG examination was not so appropriate as that of McComas et al., Calcaianu and I² concluded that in some cases of central atrophy (especially those occurring with parietal tumours), spinal motoneurons released from the control of the parietal trophic centre may be disturbed.     

On the Mechanism of Action of <Emphasis Type="Italic">lac</Emphasis> Repressor

Chen et al. have proved conclusively that lac repressor and RNA polymerase bind independently to wild type lac DNA in vitro. To explain the lacp ^s mutation, which causes competitive binding between repressor and polymerase, they suggest that a new promoter site has been created near the lac operator.     

Outcomes of a ‘One Health’ Monitoring Approach to a Five-Year Beaver (Castor fiber) Reintroduction Trial in Scotland

Recent advances in noninvasive detection methods for mycobacterial infection in primates create new opportunities for exploring the epidemiology of tuberculosis in free-living species. Chimpanzees (Pan troglodytes schweinfurthii) and baboons (Papio anubis) in Gombe National Park, Tanzania, were screened for infection with pathogens of the Mycobacterium tuberculosis Complex using Fecal IS6110 PCR; none was positive. This study demonstrates the feasibility of large-scale mycobacterial screening in wild primates.     

Quinacrine Fluorescence Patterns and Terminal DNA Labelling of Human <Emphasis Type="Italic">C</Emphasis> Group Chromosomes

THE human C group chromosomes have been difficult to study because they have rather similar morphology. Application of the quinacrine fluorescent staining technique developed by Caspersson et al.¹ now allows the identification of individual chromosomes and of the chromosome segments involved in translocations because the fluorescent patterns are not altered by the translocation^2–4. We have reported the value of this technique in analysing abnormalities of the D⁴ and G³ groups. We report here a variety of structural changes of C group chromosomes which have been characterized in this way, as well as the terminal DNA replication pattern of the C group chromosomes.     

Seed Dispersal by Primates and Implications for the Conservation of a Biodiversity Hotspot,the Atlantic Forest of South America

Primates play a fundamental role as seed dispersers, particularly in tropical rainforests. Because defaunation and fragmentation are leading several primate species to local extinction, it is fundamental to understand the role of primates as effective seed dispersers. Here we present a systematic review of studies of seed dispersal by primates in a biodiversity hotspot, the Atlantic Forest of South America, to 1) highlight gaps in our knowledge, 2) determine species richness and proportion of seed species dispersed, and 3) test the relationship between primate body size and the size of dispersed species. Our review found 79 studies of the diet of six ecospecies (Callithrix, Leontopithecus, Callicebus, Sapajus, Alouatta, Brachyteles) but only 20 of these report information on seed dispersal, and none of these are on Callithrix or Callicebus. We found a strong bias in the distribution of species and regions, with most of the studies concentrated in southeastern Brazil. All ecospecies dispersed a large proportion of the seed species they handled (72.1–93.6%). Brachyteles dispersed the highest diversity of plants (N = 73), followed by Sapajus (N = 66), Leontopithecus (N = 49), and Alouatta (N = 26). Although we found no significant relationship between primate body size and the size of seeds dispersed, Brachyteles disperse a higher diversity of large-seeded species than smaller-bodied primates. These results suggest that the local extinction of large primate species may lead to dramatic changes in the plant community, as many large-seeded plants are inaccessible to smaller arboreal frugivores. We propose guidelines for future research on primate seed dispersal to enable the evaluation of seed dispersal effectiveness and to improve our understanding of the fundamental role of primates in this key ecosystem process.     

The status of <Emphasis Type="Italic">Her2</Emphasis> amplification and <Emphasis Type="Italic">Kras</Emphasis> mutations in mucinous ovarian carcinoma

Jayson GC et al. remarked in Lancet that nearly 100% of mucinous ovarian cancer cases have Kras mutation as well as a high frequency of Her2 amplification. Using the Abbott PathVysion Her2 DNA Probe Kit and Kras mutant-enriched PCR Kits (FemtoPath®), 21 samples of primary ovarian mucinous cystadenocarcinomas from Taiwanese patients were examined to determine the status of Her2 amplification and Kras mutations. Our results showed the Her2 amplification rates were 33.33%, while the Kras mutation rates were 61.90%. We present here our results in order to enlighten the readership that the ~100% Kras mutant frequency and the high Her2 amplification rate reported by Jayson et al. may be too exaggerated to be applicable into all populations. Additionally, we report another 2 novel Kras mutations (A11V, V14I).     

Infectious Diseases in Free-Ranging Blonde Capuchins, <Emphasis Type="Italic">Sapajus flavius,</Emphasis> in Brazil

The main threats to primates worldwide are the degradation, fragmentation, and loss of their habitats; hunting (especially for bushmeat); and illegal trade. For many species, the most important threat is forest fragmentation, resulting in small populations that are restricted to isolated forest patches. In this situation, primates are particularly vulnerable to disease. The Endangered blonde capuchin (Sapajus flavius) is now restricted to a few forest patches in Northeast Brazil. We investigated the occurrence of parasites and bacterial diseases in one of three free-ranging groups of S. flavius in a small forest patch in Paraíba state, Northeast Brazil. We tested for antibodies against Leishmania spp., Trypanosoma cruzi, Toxoplasma gondii, Leptospira spp. (24 strains), and Brucella spp.. We used molecular analysis to detect Plasmodium spp., and evaluated blood smears for the presence of hemoparasites. All individuals tested negative for Leptospira spp. and B. abortus, but 8 of 48 (16%) presented antibodies for both Leishmania spp. and T. cruzi. We identified antibodies to T. gondii in 12% of the individuals tested. Plasmodium brasilianum infection was present in 4% of the individuals tested, and blood smears showed microfilariae parasites in 46% of the individuals tested. The occurrence of these infectious diseases in S. flavius may pose a significant threat in terms of reduced recruitment and poor survival rates, and an understanding of the influence of pathogens is crucial for the management of small populations of primates.     

Interaction profile-based protein classification of death domain

Background

The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experimental and computational efforts on the creation and analysis of information derived from 3D structure. In particular, the high-throughput generation of protein-protein interaction data from a few organisms makes such an approach very important towards understanding the molecular recognition that make-up the entire protein-protein interaction network. Since the generation of sequences, and experimental protein-protein interactions increases faster than the 3D structure determination of protein complexes, there is tremendous interest in developing in silico methods that generate such structure for prediction and classification purposes. In this study we focused on classifying protein family members based on their protein-protein interaction distinctiveness. Structure-based classification of protein-protein interfaces has been described initially by Ponstingl et al. [1] and more recently by Valdar et al. [2] and Mintseris et al. [3], from complex structures that have been solved experimentally. However, little has been done on protein classification based on the prediction of protein-protein complexes obtained from homology modeling and docking simulation.

Results

We have developed an in silico classification system entitled HODOCO (Homology modeling, Docking and Classification Oracle), in which protein Residue Potential Interaction Profiles (RPIPS) are used to summarize protein-protein interaction characteristics. This system applied to a dataset of 64 proteins of the death domain superfamily was used to classify each member into its proper subfamily. Two classification methods were attempted, heuristic and support vector machine learning. Both methods were tested with a 5-fold cross-validation. The heuristic approach yielded a 61% average accuracy, while the machine learning approach yielded an 89% average accuracy.

Conclusion

We have confirmed the reliability and potential value of classifying proteins via their predicted interactions. Our results are in the same range of accuracy as other studies that classify protein-protein interactions from 3D complex structure obtained experimentally. While our classification scheme does not take directly into account sequence information our results are in agreement with functional and sequence based classification of death domain family members.

     

Addenda to the Revisions of the Genera <Emphasis Type="Italic">Gergithus</Emphasis> Stål and <Emphasis Type="Italic">Hemisphaerius</Emphasis> Schaum (Hemiptera,Auchenorrhyncha, Fulgoroidea: Issidae)

The genus Gnezdilovius Meng, Webb et Wang, 2017 is revised. Maculergithus Constant et Pham, 2016, which was described as a subgenus of Gergithus Stål, 1870, is upgraded to a genus. Ishiharanus Hori, 1969 is reinstalled from synonymy with Gergithus and considered a valid name. Two new genera are erected, Ceratogergithus Gnezdilov, gen. n. (type species: Gergithus spinosus Che, Zhang et Wang, 2007) and Ophthalmosphaerius Gnezdilov, gen. n. (type species: Hernisphaerius trilobulus Che, Zhang et Wang, 2006). Hernisphaerius bistriatus Schumacher, 1915, Gergithus carbonarius Melichar, 1906, G. rosticus Chan et Yang, 1994, G. nummarius Chan et Yang, 1994, and G. rotundus Chan et Yang, 1994 are transferred to the genus Epyhemisphaerius Chan et Yang, 1994, Gergithus quinquemaculatus Che, Zhang, Wang, 2007—to the genus Maculergithus, Gergithus chelatus Che, Zhang, Wang, 2007 and G. pseudotessellatus Che, Zhang, Wang, 2007—to the genus Ceratogergithus, Hernisphaerius binocularis Chen, Zhang, Chang, 2014—to the genus Ophthalmosphaerius, and Gergithus robustus hoozanensis Schumacher, 1915—to the genus Gnezdilovius. The male genitalia of Gergithus herbaceus (Kirby, 1891) and Hernisphaerius interclusus Noualhier, 1896 are illustrated for the first time.     

Regulatory Properties of Intergeneric Hybrids of Aspartate Transcarbamylase

THE regulatory enzyme aspartate transcarbamylase (ATCase) from Escherichia coli contains two non-identical protein sub-units, one the catalytic subunit which provides the active sites of the enzyme and the other the regulatory subunit which provides the binding sites for nucleotide inhibitors and activators^1,2. The catalytic subunit is a trimer of “C” polypeptide chains, associated by three heterologous c: c domains of bonding (terminology given by Monod et al.³ and Cohlberg et al.⁴). The regulatory subunit is a dimer of “R” chains, associated by an isologous r: r domain. Two catalytic and three regulatory subunits interact specifically across six r: c domains of inter-subunit bonding to complete the quaternary structure of the ATCase molecule.     

New and little known orthopteroid insects (Polyneoptera) from fossil resins: Communication 3

New taxa of Orthoptera Ensifera are described in the families Mogoplistidae [Protomogoplistes asquamosus gen. et sp. nov. (Upper Cretaceous) in the subfamily Protomogoplistinae subfam. nov. and Archornebius balticus gen. et sp. nov. (Eocene), Pseudarachnocephalus gen. nov., P. dominicanus sp. nov., and P. latiusculus sp. nov. (all Miocene) in Mogoplistinae] and Gryllidae [Eopentacentrus borealis gen. et sp. nov. (Eocene), ?Grossoxipha feminea sp. nov. (Miocene), and Apentacentrus copalicus sp. nov. in the subfamily Pentacentrinae, ?Cyrtoxipha electrina sp. nov. and ?Cyrtoxipha illegibilis sp. nov. (both Miocene) in Trigonidiinae, and Baltonemobius fossilis gen. et sp. nov. (Eocene) in Nemobiinae]. The Miocene genera Proanaxipha Vickery et Poinar and Grossoxipha Vickery et Poinar are transferred from the subfamily Trigonidiinae to Pentacentrinae. P. latoca Vickery et Poinar and Abanaxipha longispina Vickery et Poinar are redescribed; the male of the latter species is described for the first time.     

First evidence of epizoochorous seed dispersal by golden snub-nosed monkeys (<Emphasis Type="Italic">Rhinopithecus roxellana</Emphasis>) in temperate forest

Although many primates are identified as effective endozoochorous seed dispersers in forest ecosystems, epizoochorous seed dispersal by primates has generally been overlooked. In this study, we report epizoochorous seed dispersal in a group of free-ranging golden snub-nosed monkeys (Rhinopithecus roxellana) residing in the temperate forests of central China by identifying seeds carried by 12 well-habituated individuals. The results showed a total of 1920 seeds (five families, seven genera) belonging to eight plant species attached to the monkeys’ fur; the three most abundant species were Geum aleppicum (54% of the total), Torilis japonica (17%), and Agrimonia pilosa (14%). The majority of seeds (95.3%) that attached to the monkeys’ fur had special morphologies such as hairs, hooks, or awns. We also found that the quantity of seeds attached to the fur was not significantly different by age-sex class, even though adult males have very long fur. Our study provides the first empirical evidence of epizoochorous seed dispersal by primates and suggests the role of primates in seed dispersal may be greater than previously assumed.     

Contribution to the knowledge of the weevil genus <Emphasis Type="Italic">Otiorhynchus</Emphasis> Germ. (Coleoptera,Curculionidae) from Turkmenistan and adjacent territories

Data on 15 species of the subgenus Pseudotiorhynchus Magnano, 2004 of the genus Otiorhynchus Germar, 1822 from Kazakhstan, Turkmenistan, and Iran are given. Otiorhynchus lukarevskayae Davidian, sp. n., O. karakalensis Davidian et Savitsky, sp. n., O. konstantini Davidian et Savitsky, sp. n., O. muratovi Savitsky et Davidian, sp. n., O. kopetdagicus Savitsky et Davidian, sp. n., and O. shakhensis Savitsky et Davidian, sp. n. from Turkmenistan, and O. khorasanus Savitsky et Davidian, sp. n. from Iran are described as new to science. A new synonymy is established: Pseudotiorhynchus Magnano, 2004 = Crassorhynchus Magnano, 2004, syn. n. Otiorhynchus iranensis Magnano, 2004 is transferred from the subgenus Protarammichnus Voss, 1960 to the subgenus Pseudotiorhynchus. Lectotype of O. conicirostris Stierlin, 1886 is designated. A key to 15 species of the subgenus Pseudotiorhynchus is given. The new subgenus Microhanibotus Savitsky et Davidian, subgen. n. is established for the new species O. ghilarovi Davidian et Savitsky, sp. n. from the Western Kopet Dagh in Turkmenistan. Microhanibotus subgen. n. is closely related to the subgenera Pseudotiorhynchus, Hanibotus Reitter, 1912 and Nubidanus Reitter, 1912.     

New data on the fauna and systematics of Palaearctic species of the click-beetle subfamily Agrypninae Candèze, 1857 (Coleoptera,Elateridae)

New data on the distribution and taxonomy of some Palaearctic species of click-beetles of the subfamily Agrypninae are given. The external morphology and genitalia of the previously unknown females of Compsolacon korotjaevi Gur. and C. agrestis (Vats et Kash.) comb. n. are described. Several taxa are recorded from the following territories for the first time: the genus Eumoeus Cand. from the Palaearctic Region, the species Compsolacon agrestis comb. n. and C. himalayanus Jag. from Afghanistan, Compsolacon turkestanicus (Schw.) from Kyrgyzstan and Afghanistan, Danosoma conspersum (Gyll.) from Kazakhstan, Lacon quadrinodatus Lew. from Russia, and L. unicolor (Cand.) from Iraq. Several Northern Indian species of Agrypnus Esch. are transferred to Compsolacon Rtt., and their systematic positions are briefly discussed: C. agrestis, C. inlustris (Vats et Kash.), C. jacksoni (Vats et Kash.), C. kuluensis (Vats et Kash.), C. maisus (Vats et Kash.), C. planocorpus (Vats et Kash.), C. rameshi (Vats et Kash.), C. repercussus (Vats et Kash.), C. solanensis (Vats et Kash.), C. souslapisus (Vats et Kash.), C. subargillus (Vats et Kash.), C. subfaenum (Vats et Kash.) and C. sublapideus (Vats et Kash.) (all comb. n.). The following new combinations are also established: Compsolacon aequalis (Cand.) comb. n. and Compsolacon brachychaetus (Kollar) comb. n. (both ex Lacon). The following new synonymies are established: Lacon funebris (Sols.) = Adelocera grisea Schw., syn. n.; = Adelocera incompta Kr., syn. n.; Eumoeus murrayi Cand. = Tetralobus quadrifoveatus Vats et Kash., syn. n.     

Taxonomy and Diversity of Freshwater Bivalve Mollusks (Bivalvia) of China (Based on Analysis of the Catalog by He and Zhuang, 2013)

The diversity of freshwater Bivalvia in China was assessed on the basis of critical analysis of original and published data on the fauna, morphology, taxonomy, and molecular genetics of this group. The taxonomic composition of the following genera has been considered in depth: Anemina Haas 1969, Cristaria Schumacher 1817, Sinanodonta Modell 1944, Lanceolaria Conrad 1853, Middendorffinaia Moskvicheva et Starobogatov 1973, Nodularia Conrad 1853, Unio Philipsson in Retzius 1788, Inversidens Haas 1911, Sphaerium Scopoli 1777, Pisidium Pfeiffer 1821, Odhneripisidium Kuiper 1962, and Euglesa Leach in Jenyns 1832 = Cyclocalyx Dall 1905. No fewer than 170 bivalve species were demonstrated to occur in the freshwater areas of China. Underestimation of the Bivalvia species abundance in previous studies, including the latest catalog of the Chinese Bivalvia (He and Zhuang, 2013), may be accounted for mostly by inadequate use of morphological methods and limited faunistic data, as well as a little number of taxonomic works supported by molecular data. Both the generic and specific compositions of the Chinese Unioniformes and Luciniformes have been significantly extended and updated. Based on a complex study of conchological characters, the following synonymy was established for three species: Sinanodonta qingyuani He et Zhuang 2013 = S. woodiana (Lea 1834) syn. n., Lanceolaria yueyingae He et Zhuang 2013 = L. eucylindrica C. Lin 1962 syn. n., Acuticosta jianghanensis He et Zhuang 2013 = Nodularia douglasiae (Griffith et Pidgeon 1833) syn. n.