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Fulltext A new species of the Cyrtodactylusquadrivirgatus complex (Chordata, Reptilia, Squamata, Gekkonidae) from Sumatra Barat, Indonesia

Ahda Y, Nugraha FAD, Hon Tjong D, Kurniawan N, Amardi Y, Fauzi MA, et al.

Zookeys, 2023;1168:367-386.
PMID: 37448483 DOI: 10.3897/zookeys.1168.98724

Among the six species of Cyrtodactylus occurring in Sumatra, two species were described based on non-Sumatran type series, C.consobrinus and C.quadrivirgatus. The latter species was described originally from Thailand thus the wider distribution in Sumatra should be clarified taxonomically. Cyrtodactylusquadrivirgatus from Sumatra Barat was examined using both morphology and the Natrium Dehydrogenase Subunit 2 (ND2) gene to clarify its taxonomic status and phylogenetic placement. It was found that these specimens form a sister clade to all other species of the sworderi group from Peninsular Malaysia and the genetic distance ranges from 20-24.3%. This subset is herein described as a new species. The new species is readily distinguished from C.quadrivirgatus and other Sumatran species by a combination of characters: small size SVL 37.5-53.78 mm; longitudinal rows of dorsal tubercles 16-19; paravertebral tubercles 31-41; ventral scales 32-43; 24-49 enlarged precloacal and femoral scales; precloacal pores rarely present; no precloacal depression; two postcloacal tubercles on each side; 14-19 subdigital lamellae on forth toe; 9-15 supralabial scales; 9-12 infralabial scales; three or four internasal scales; and 3-6 gular scales that border the first pair of postmental scales. This work underscores the importance of clarifying widely distributed species for taxonomic validation.
Fulltext Common but ignored: a new species of Cyrtodactylus (Chordata, Reptilia, Squamata, Gekkonidae) from lowland Sumatra Barat, Indonesia

Nugraha FAD, Ahda Y, Tjong DH, Kurniawan N, Riyanto A, Fauzi MA, et al.

Zookeys, 2023;1169:47-64.
PMID: 38328028 DOI: 10.3897/zookeys.1169.98681

The lowland region of Sumatra Barat has received little attention in previous biodiversity studies. Past studies have mainly focused on highland habitat and conservation areas. However, many populations of Cyrtodactylus in the lowland habitats of Sumatra Barat were not correctly identified. A phylogenetic tree based on the NADH dehydrogenase subunit 2 (ND2) gene showed that the lowland Sumatran population is the sister group of the Malaysian lowland species, C.semenanjungensis, together nesting within the agamensis group. The genetic divergence within the Sumatra Barat population is 0-4.2% and 18.3-20% to C.semenanjungensis. Further examination of morphological characters revealed that they differed from the sister clade and other Sumatran Cyrtodactylus members by a unique combination of characters such as absence of tubercle on brachium, presence of tubercle on ventrolateral fold, 32-41 paravertebral tubercles, 38-46 ventral scales, enlarged femoral scales, presence of precloacofemoral pores and 22-23 subdigital lamellae under fourth toe. Based on the morphological and molecular evidence, the lowland Sumatran population is herein described as a new species, increasing the number of species in Sumatra to seven. More comprehensive and intensive sampling efforts would most likely yield further discoveries in the group of Sumatran Cyrtodactylus in the near future.
Fulltext Genetic and morphological analyses of Gracilaria firma and G. changii (Gracilariaceae, Rhodophyta), the commercially important agarophytes in western Pacific

Ng PK, Lin SM, Lim PE, Hurtado AQ, Phang SM, Yow YY, et al.

PLoS One, 2017;12(7):e0182176.
PMID: 28759629 DOI: 10.1371/journal.pone.0182176

Many studies classifying Gracilaria species for the exploitation of agarophytes and the development of the agar industry were conducted before the prevalence of molecular tools, resulting in the description of many species based solely on their morphology. Gracilaria firma and G. changii are among the commercially important agarophytes from the western Pacific; both feature branches with basal constrictions that taper toward acute apices. In this study, we contrasted the morpho-anatomical circumscriptions of the two traditionally described species with molecular data from samples that included representatives of G. changii collected from its type locality. Concerted molecular analyses using the rbcL and cox1 gene sequences, coupled with morphological observations of the collections from the western Pacific, revealed no inherent differences to support the treatment of the two entities as distinct taxa. We propose merging G. changii (a later synonym) into G. firma and recognize G. firma based on thallus branches with abrupt basal constrictions that gradually taper toward acute (or sometimes broken) apices, cystocarps consisting of small gonimoblast cells and inconspicuous multinucleate tubular nutritive cells issuing from gonimoblasts extending into the inner pericarp at the cystocarp floor, as well as deep spermatangial conceptacles of the verrucosa-type. The validation of specimens under different names as a single genetic species is useful to allow communication and knowledge transfer among groups from different fields. This study also revealed considerably low number of haplotypes and nucleotide diversity with apparent phylogeographic patterns for G. firma in the region. Populations from the Philippines and Taiwan were divergent from each other as well as from the populations from Malaysia, Thailand, Singapore and Vietnam. Establishment of baseline data on the genetic diversity of this commercially important agarophyte is relevant in the context of cultivation, as limited genetic diversity may jeopardize the potential for its genetic improvement over time.
Fulltext Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae

Ng PK, Lin SM, Lim PE, Liu LC, Chen CM, Pai TW

BMC Genomics, 2017 Jan 06;18(1):40.
PMID: 28061748 DOI: 10.1186/s12864-016-3453-0

BACKGROUND: The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined.
RESULTS: The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support.
CONCLUSIONS: Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto.
Fulltext Phase III HEAT Study Adding Lyso-Thermosensitive Liposomal Doxorubicin to Radiofrequency Ablation in Patients with Unresectable Hepatocellular Carcinoma Lesions

Tak WY, Lin SM, Wang Y, Zheng J, Vecchione A, Park SY, et al.

Clin Cancer Res, 2018 01 01;24(1):73-83.
PMID: 29018051 DOI: 10.1158/1078-0432.CCR-16-2433

Purpose: Lyso-thermosensitive liposomal doxorubicin (LTLD) consists of doxorubicin contained within a heat-sensitive liposome. When heated to ≥40°C, LTLD locally releases a high concentration of doxorubicin. We aimed to determine whether adding LTLD improves the efficacy of radiofrequency ablation (RFA) for hepatocellular carcinoma (HCC) lesions with a maximum diameter (dmax) of 3 to 7 cm.Experimental Design: The HEAT Study was a randomized, double-blind, dummy-controlled trial of RFA ± LTLD. The 701 enrolled patients had to have ≤4 unresectable HCC lesions, at least one of which had a dmax of 3 to 7 cm. The primary endpoint was progression-free survival (PFS) and a key secondary endpoint was overall survival (OS). Post hoc subset analyses investigated whether RFA duration was associated with efficacy.Results: The primary endpoint was not met; in intention-to-treat analysis, the PFS HR of RFA + LTLD versus RFA alone was 0.96 [95% confidence interval (CI), 0.79-1.18; P = 0.71], and the OS HR ratio was 0.95 (95% CI, 0.76-1.20; P = 0.67). Among 285 patients with a solitary HCC lesion who received ≥45 minutes RFA dwell time, the OS HR was 0.63 (95% CI, 0.41-0.96; P < 0.05) in favor of combination therapy. RFA + LTLD had reversible myelosuppression similar to free doxorubicin.Conclusions: Adding LTLD to RFA was safe but did not increase PFS or OS in the overall study population. However, consistent with LTLD's heat-based mechanism of action, subgroup analysis suggested that RFA + LTLD efficacy is improved when RFA dwell time for a solitary lesion ≥45 minutes. Clin Cancer Res; 24(1); 73-83. ©2017 AACR.