scholarly journals Taxonomic status of the nominal forms assigned to Necromys lactens (Rodentia, Cricetidae) as revealed by molecular and morphometric evidence

2019 ◽  
Vol 101 (1) ◽  
pp. 24-35
Author(s):  
J Pablo Jayat ◽  
Pablo E Ortiz ◽  
Guillermo D’Elía ◽  
Jorge Salazar-Bravo ◽  
Bruce D Patterson
Keyword(s):  
Taxonomic Status ◽  
High Elevation ◽  
Integrative Framework ◽  
South Central ◽  
Morphometric Analyses ◽  
Extant Species ◽  
Base Pair Fragment ◽  
América Del Sur ◽  
Genus One ◽  
Pair Fragment

Abstract Necromys is a genus of sigmodontine rodent that inhabits grasslands and scrublands in South America. Eight extant species are recognized in the genus; one of these is Necromys lactens, which inhabits high-elevation grasslands in the Yungas from south-central Bolivia to northwestern Argentina. Morphological variation in N. lactens has been recognized by the description of three nominal forms. Geographically structured genetic diversity also has been observed, but a thorough revision of these nominal forms within an integrative framework has yet to be performed. We conducted a phylogeographic assessment based on an 801 base-pair fragment of the cytochrome-b gene that guided morphometric analyses (univariate and multivariate comparisons) of patterns of geographic variation in the species, and the distinction of its nominal forms. Haplotypes of N. lactens form a well-supported and geographically structured clade. Within it, there are two main clades; haplotypes from the northern range form a well-supported clade, sister and allopatric to a weakly supported southern clade, which includes variants collected at or near the type localities of three nominal forms. In turn, both main clades are composed by two allopatric subclades. Morphometric analyses indicated no differences in shape of the skull among the three nominal forms or between the recovered clades and subclades. Taking together all the available evidence, we consider N. lactens to be a monotypic species. Necromys es un género de roedor sigmodontino que habita los pastizales y arbustales de América del Sur. Se reconocen ocho especies actualmente en existencia en el género; una de ellas, Necromys lactens, habita pastizales de altura en las Yungas, desde el centro-sur de Bolivia hasta el noroeste de Argentina. Se ha reconocido variación morfológica en N. lactens con base en descripciones de tres formas nominales; también se ha observado diversidad genética geográficamente estructurada, pero una revisión exhaustiva de esas formas nominales dentro de un esquema integrativo aún no se ha llevado a cabo. Realizamos una evaluación filogeográfica basada en un fragmento de 801 pares de bases del gen citocromo b que orientó análisis morfométricos (comparaciones univariadas y multivariadas) respecto al patrón geográfico de variación de la especie y la distinción de sus formas nominales. Los haplotipos de N. lactens forman un clado bien apoyado y geográficamente estructurado. Dentro de este clado, los haplotipos del norte de su área de distribución forman un clado bien apoyado que es hermano y alopátrico con respecto de un clado austral débilmente apoyado, el cual incluye variantes colectadas en las localidades tipo de las tres formas nominales o sus cercanías. A su vez, ambos clados principales están compuestos por dos sub-clados alopátricos. Los análisis morfométricos no revelaron diferencias en la forma del cráneo entre las tres formas nominales ni entre los clados y sub-clados recuperados. Teniendo en cuenta toda la evidencia disponible, consideramos que N. lactens es una especie monotípica.

Two systems of glucose repression of the GAL1 promoter in Saccharomyces cerevisiae

1990 ◽  
Vol 10 (9) ◽  
pp. 4757-4769
Author(s):  
J S Flick ◽  
M Johnston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Base Pair ◽  
Glucose Repression ◽  
Gene Products ◽  
Gal1 Promoter ◽  
Base Pair Fragment ◽  
Common Signal ◽  
Multiple Sequences ◽  
Pair Fragment ◽  
Gal1 Gene

Expression of the GAL1 gene in Saccharomyces cerevisiae is strongly repressed by growth on glucose. We show that two sites within the GAL1 promoter mediate glucose repression. First, glucose inhibits transcription activation by GAL4 protein through UASG. Second, a promoter element, termed URSG, confers glucose repression independently of GAL4. We have localized the URSG sequences responsible for glucose repression to an 87-base-pair fragment located between UASG and the TATA box. Promoters deleted for small (20-base-pair) segments that span this sequence are still subject to glucose repression, suggesting that there are multiple sequences within this region that confer repression. Extended deletions across this region confirm that it contains at least two and possibly three URSG elements. To identify the gene products that confer repression upon UASG and URSG, we have analyzed glucose repression mutants and found that the GAL83, REG1, GRR1, and SSN6 genes are required for repression mediated by both UASG and URSG. In contrast, GAL82 and HXK2 are required only for UASG repression. A mutation designated urr1-1 (URSG repression resistant) was identified that specifically relieves URSG repression without affecting UASG repression. In addition, we observed that the SNF1-encoded protein kinase is essential for derepression of both UASG and URSG. We propose that repression of UASG and URSG is mediated by two independent pathways that respond to a common signal generated by growth on glucose.

P2X(4) purinoceptors mediate an ATP-activated, non-selective cation current in rabbit osteoclasts

1999 ◽  
Vol 112 (23) ◽  
pp. 4425-4435 ◽  
Author(s):  
L.N. Naemsch ◽  
A.F. Weidema ◽  
S.M. Sims ◽  
T.M. Underhill ◽  
S.J. Dixon
Keyword(s):  
Outward Current ◽  
Osteoclast Formation ◽  
Extracellular Nucleotides ◽  
Patch Clamp Recording ◽  
Inward Current ◽  
Reverse Transcription Pcr ◽  
Cation Current ◽  
Degenerate Oligonucleotide ◽  
Base Pair Fragment ◽  
Pair Fragment

Extracellular nucleotides act as signaling molecules in numerous tissues. In bone, nucleotides stimulate osteoclast formation and activity; however, the receptors and signaling mechanisms underlying these effects have yet to be identified. To identify specific P2X purinoceptor subtypes in osteoclasts, degenerate oligonucleotide primers were used to PCR-amplify DNA fragments from a rabbit osteoclast cDNA library. A 372-base-pair fragment was obtained that encoded an amino acid sequence with 88% identity to the rat P2X(4) purinoceptor. The presence of P2X(4) mRNA in purified osteoclasts was confirmed by reverse transcription-PCR. Endogenous purinoceptors were functionally characterized in isolated rabbit osteoclasts by patch-clamp recording in whole-cell configuration. At negative membrane potentials, application of ATP or ADP rapidly activated an inward current followed by an outward current. In contrast, UTP or ADPbetaS elicited only an outward current, due to activation of a Ca(2+)-dependent K(+) conductance. The initial inward current was non-selective for cations and inactivated during agonist application. Furthermore, the inward current was insensitive to suramin and Cibacron blue, and was potentiated by Zn(2+). These characteristics are consistent with properties of P2X(4) purinoceptors. Activation of P2X(4) purinoceptors leads to cation influx and depolarization. Nucleotides, released at sites of trauma or inflammation, may act through these receptors on osteoclasts to stimulate bone resorption.

Transcriptional control signals of a herpes simplex virus type 1 late (gamma 2) gene lie within bases -34 to +124 relative to the 5' terminus of the mRNA

1986 ◽  
Vol 6 (11) ◽  
pp. 3652-3666
Author(s):  
F L Homa ◽  
T M Otal ◽  
J C Glorioso ◽  
M Levine
Keyword(s):  
Herpes Simplex ◽  
Dna Sequences ◽  
Viral Dna ◽  
Regulated Expression ◽  
Base Pair Fragment ◽  
Simplex Virus ◽  
Pair Fragment ◽  
Gc Gene ◽  
Hsv 1

The cis-acting DNA sequences required for regulated expression of a herpes simplex virus type 1 (HSV-1) late (gamma 2) gene were studied by using viruses containing specific deletions in the 5' transcribed noncoding and upstream regions of the HSV-1 glycoprotein C (gC) gene, a model gamma 2 gene. Nine mutant viruses which had variable 5' and 3' deletions within bases -569 to +124 relative to the 5' terminus of the gC mRNA were isolated. The mutants were isolated by a simple in situ hybridization screening procedure not requiring any prior selective pressure for or against expression of the gC gene. Analysis of RNA extracted from cells infected with individual mutants showed that the DNA sequences required for regulated expression of this gamma 2 gene lay within bases -34 to +124. This 158-base-pair fragment was sufficient to confer accurate and quantitative expression of gC mRNA and to maintain the stringent requirement on viral DNA replication for expression of this gene. Moreover, it was found that sequences located between -34 and +14 contained signals essential for expression of gC. To determine whether the -34 to +124 sequences would function as a gamma 2 promoter when moved to another region of the HSV-1 genome, the 158-base-pair fragment was substituted for the normal thymidine kinase promoter-regulatory sequences in the thymidine-kinase gene locus. Transcription of this chimeric gene was regulated as a gamma 2 gene in that its expression in infected cells was dependent on viral DNA synthesis. The only recognizable consensus sequence upstream of the transcription initiation site for this gene was the TATAAA sequence at -30.

Taxonomic review of two fossil crocodylians from the Cenozoic of South America and its implications for the crocodylian fauna of the continent

Zootaxa ◽  
2019 ◽  
Vol 4656 (3) ◽  
pp. 475-486
Author(s):  
GIOVANNE M. CIDADE ◽  
DANIEL FORTIER ◽  
ASCANIO DANIEL RINCÓN ◽  
ANNIE SCHMALTZ HSIOU
Keyword(s):  
South America ◽  
Fossil Record ◽  
Middle Miocene ◽  
Taxonomic Status ◽  
Junior Synonym ◽  
Diverse Group ◽  
Taxonomic Review ◽  
Nomen Dubium ◽  
Extant Species ◽  
The World

The crocodylomorph fauna of the Cenozoic of South America is one of the richest and most diverse in the world. The most diverse group within that fauna is Alligatoroidea, with nearly all of its species belonging to the Caimaninae clade. Many of the fossil alligatoroid species from the Cenozoic of South America were proposed based on very incomplete remains, and as a result their validity requires revision. Two such species are Balanerodus logimus Langston, 1965, from the middle Miocene of Colombia and Peru, and Caiman venezuelensis Fortier & Rincón, 2012, from the Pliocene-Pleistocene of Venezuela. This study has performed a thorough review of the taxonomic status of these two alligatoroid species, concluding that B. logimus is a nomen dubium and that Ca. venezuelensis is a junior synonym of the extant species Ca. crocodilus. This review offers a significantly more accurate scenario for alligatoroid diversity in the Cenozoic of South America in different epochs such as the Miocene and Pleistocene. Additionally, the record of Ca. crocodilus from the Pleistocene of Venezuela is the first fossil record that can be assigned to this species. 

scholarly journals Sequence Analysis of the K13-Propeller Gene in Artemisinin Challenging Plasmodium falciparum Isolates from Malaria Endemic Areas of Odisha, India: A Molecular Surveillance Study

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Ramakanta Rana ◽  
Manoranjan Ranjit ◽  
Madhusmita Bal ◽  
Hemant Kumar Khuntia ◽  
Sanghamitra Pati ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Hot Spots ◽  
Reference Sequence ◽  
Nested Polymerase Chain Reaction ◽  
Molecular Surveillance ◽  
Base Pair Fragment ◽  
Baseline Information ◽  
Polymerase Chain ◽  
Dna Alignment ◽  
Pair Fragment

Estimation of the spread and advancement of Plasmodium falciparum artemisinin-resistant parasites can be done by probing polymorphisms in the kelch (Pfk13) domain (a validated molecular marker). This study aimed to provide baseline information for future artemisinin surveillance by analyzing the k13-propeller domain in P. falciparum field isolates collected from 24 study areas in 14 malaria hot spots of Odisha (previously Orissa) during July 2018-January 2019. A total of 178 P. falciparum mono infections were assessed. An 849-base pair fragment encoding the Pfk13 propeller was amplified by nested polymerase chain reaction and sequenced in both directions (PCR). After DNA alignment with the 3D7 reference sequence, all samples were found to be wild type. It can be anticipated that malaria public health is not under direct threat in Odisha relating to ART resistance.

Meadow Invasion from High-Elevation Spruce-Fir Forest in South-Central New Mexico

1999 ◽  
Vol 44 (4) ◽  
pp. 444 ◽  
Author(s):  
James M. Dyer ◽  
K. Evan Moffett
Keyword(s):  
New Mexico ◽  
High Elevation ◽  
South Central

scholarly journals Identification of Sugarcane Striate Mosaic-Associated Virus by Partial Characterization of Its Double-Stranded RNA

1999 ◽  
Vol 89 (10) ◽  
pp. 877-883 ◽  
Author(s):  
Yoon Gi Choi ◽  
Barry J. Croft ◽  
John W. Randles
Keyword(s):  
Double Stranded Rna ◽  
Virus Particles ◽  
Reverse Transcription Pcr ◽  
Protein Size ◽  
Putative Coat Protein ◽  
Base Pair Fragment ◽  
Potato Virus M ◽  
Polymerase Chain ◽  
Pair Fragment

Sugarcane striate mosaic (ScSM)-affected sugarcane leaves contain a disease-associated 9-kilobase (kb) double-stranded RNA (dsRNA), usually together with 6- and 2.6-kb dsRNAs. The purified 9-kb dsRNA was amplified by the randomly primed polymerase chain reaction (PCR) and cloned. The nucleotide sequences of three separate regions, representing about 2.55 kb (28%) of the dsRNA sequence, were found to have significant similarities to viruses in the genera Capillo-, Carla-, Fovea-, Potex-, Poty-, Tricho-, and Tymovirus. Greatest overall similarity was found to apple stem pitting virus, with less similarity to blueberry scorch virus and potato virus M. A standard virus purification procedure was used to identify slightly flexuous filamentous particles that copurified with the disease-associated RNA. Particle modal lengths were approximately 950 and 1,900 nm with a diameter of 15 nm. Preparations contained a 51-kDa putative capsid protein and a 9-kb single-stranded RNA with a probable 3′ polyadenylate tract. These ScSM-associated virus particles differ physically from viruses in existing genera because of their relative rigidity, length, and putative coat protein size. Reverse-transcription PCR with a primer pair designed from the sequenced segments amplified a 820-base pair fragment from ScSM-affected but not healthy sugarcane plants.

scholarly journals Genus Apodemus in the Pleistocene of Central Europe: when did the extant taxa appear?

2017 ◽  
Vol 73 (3-4) ◽  
pp. 460-481 ◽  
Author(s):  
Markéta Knitlová ◽  
Ivan Horáček
Keyword(s):  
Central Europe ◽  
Taxonomic Status ◽  
Early Pleistocene ◽  
Middle Pleistocene ◽  
Morphometric Characteristics ◽  
Variation Pattern ◽  
Fossil Species ◽  
The Czech Republic ◽  
Extant Species ◽  
Late Middle Pleistocene

Abstract The extant species of the genus Apodemus represent the most common small mammals of Central Europe. Unfortunately, their phylogenetic past is only poorly known. With the aid of detailed biometric analyses we tried to identify the first appearance of the phenotypic patterns characterizing the extant populations. We examined dental material of Apodemus from 53 community samples from the territory of the Czech Republic and Slovakia dated from the early Villanyian (MN 16/17) to the late Middle Pleistocene (Q 3) with particular respect to their correspondence with the morphometric characteristics of the extant species. While the Toringian (Q 3) interglacial samples invariably include forms identical with the extant taxa A. flavicollis, A. sylvaticus and supposedly A. uralensis (including the items corresponding to A. maastrichtiensis), the samples of Early Pleistocene age (MN 17 – Q 2) exhibited clear differences in the variation pattern which results in questioning the possibility of their co-identification with the respective extant species. In most instances they varied within the limits in resembling A. sylvaticus but exceeded its variation ranges in some non-metric characters. Regarding serious doubts on real taxonomic status of other named fossil species we propose to denote these Plio-Pleistocene sylvaticus-like phenotypes provisionally with the prior name A. atavus Heller, 1936.

scholarly journals Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha, Ctenomys)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9259 ◽  
Author(s):  
Pablo Teta ◽  
Guillermo D’Elía
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Subterranean Rodents ◽  
South American ◽  
Northern Patagonia ◽  
Karyological Data ◽  
Three New Species ◽  
Genus One

Ctenomys Blainville 1826 is one of the most diverse genera of South American caviomorph rodents. Currently, six species of this genus are reported from Patagonia, south of 42°S. In this contribution, we assessed the taxonomic status of several populations from eastern and central Chubut province, northern Patagonia. Based on phylogenetic analyses of DNA sequences, morphology assessment (qualitative and quantitative), and previously published karyological data, we describe three new species of this genus, one formed by two subspecies, endemic to northern Patagonia. In addition, we include C. coyhaiquensis Kelt and Gallardo 1994 into the synonymy of C. sericeus J.A. Allen 1903. Finally, we discussed the need for additional integrative approaches, including field collection of specimens, to better understand the diversity of this highly speciose rodent genus.

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